Starting phenix.real_space_refine on Sat Aug 23 23:01:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvh_17966/08_2025/8pvh_17966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvh_17966/08_2025/8pvh_17966.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/8pvh_17966/08_2025/8pvh_17966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvh_17966/08_2025/8pvh_17966.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvh_17966/08_2025/8pvh_17966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvh_17966/08_2025/8pvh_17966.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= 0.000 sd= 0.005 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 76 5.16 5 Cl 4 4.86 5 C 9684 2.51 5 N 2568 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15172 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3792 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 2.63, per 1000 atoms: 0.17 Number of scatterers: 15172 At special positions: 0 Unit cell: (105.187, 98.4555, 103.504, 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) Cl 4 17.00 S 76 16.00 O 2840 8.00 N 2568 7.00 C 9684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 584.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 45.8% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP A 136 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 137 " --> pdb=" O CYS A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 171 through 186 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 199 through 213 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 315 through 328 Processing helix chain 'A' and resid 347 through 364 Processing helix chain 'A' and resid 394 through 399 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE A 483 " --> pdb=" O GLY A 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP B 136 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 137 " --> pdb=" O CYS B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 171 through 186 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 199 through 213 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 347 through 364 Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 469 through 471 No H-bonds generated for 'chain 'B' and resid 469 through 471' Processing helix chain 'B' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE B 483 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA C 137 " --> pdb=" O CYS C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 171 through 186 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 199 through 213 Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 315 through 328 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 394 through 399 Processing helix chain 'C' and resid 413 through 423 Processing helix chain 'C' and resid 436 through 447 Processing helix chain 'C' and resid 469 through 471 No H-bonds generated for 'chain 'C' and resid 469 through 471' Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE C 483 " --> pdb=" O GLY C 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 122 through 137 removed outlier: 3.526A pdb=" N TRP D 136 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA D 137 " --> pdb=" O CYS D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 171 through 186 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 199 through 213 Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 247 through 261 removed outlier: 3.706A pdb=" N LEU D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 315 through 328 Processing helix chain 'D' and resid 347 through 364 Processing helix chain 'D' and resid 394 through 399 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 436 through 447 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 478 through 483 removed outlier: 3.911A pdb=" N PHE D 483 " --> pdb=" O GLY D 479 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=2, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE A 38 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN A 51 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A 40 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS A 193 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL A 386 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE A 309 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE A 411 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL A 311 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE A 433 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE A 277 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA A 430 " --> pdb=" O TRP A 453 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE A 381 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=8, first strand: chain 'B' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE B 38 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN B 51 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS B 193 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN B 165 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'B' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE B 309 " --> pdb=" O MET B 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE B 411 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 311 " --> pdb=" O PHE B 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE B 433 " --> pdb=" O PRO B 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 277 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA B 430 " --> pdb=" O TRP B 453 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'B' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE B 381 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=14, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS C 163 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS C 193 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL C 386 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE C 309 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE C 411 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL C 311 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE C 433 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE C 277 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 430 " --> pdb=" O TRP C 453 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'C' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE C 381 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=20, first strand: chain 'D' and resid 37 through 41 removed outlier: 6.279A pdb=" N PHE D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN D 51 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.187A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.244A pdb=" N CYS D 163 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LYS D 193 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN D 165 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 367 through 370 removed outlier: 6.533A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE D 309 " --> pdb=" O MET D 409 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE D 411 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL D 311 " --> pdb=" O PHE D 411 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N PHE D 433 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE D 277 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'D' and resid 374 through 375 removed outlier: 4.320A pdb=" N PHE D 381 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3300 1.34 - 1.46: 4508 1.46 - 1.58: 7580 1.58 - 1.70: 0 1.70 - 1.82: 108 Bond restraints: 15496 Sorted by residual: bond pdb=" CA PRO D 215 " pdb=" C PRO D 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA PRO A 215 " pdb=" C PRO A 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA PRO B 215 " pdb=" C PRO B 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA PRO C 215 " pdb=" C PRO C 215 " ideal model delta sigma weight residual 1.514 1.535 -0.021 5.50e-03 3.31e+04 1.39e+01 bond pdb=" CA SER B 185 " pdb=" CB SER B 185 " ideal model delta sigma weight residual 1.528 1.473 0.056 1.56e-02 4.11e+03 1.27e+01 ... (remaining 15491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 15716 1.85 - 3.70: 4484 3.70 - 5.55: 684 5.55 - 7.40: 84 7.40 - 9.25: 16 Bond angle restraints: 20984 Sorted by residual: angle pdb=" CA PHE D 469 " pdb=" CB PHE D 469 " pdb=" CG PHE D 469 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA PHE B 469 " pdb=" CB PHE B 469 " pdb=" CG PHE B 469 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA PHE A 469 " pdb=" CB PHE A 469 " pdb=" CG PHE A 469 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CA PHE C 469 " pdb=" CB PHE C 469 " pdb=" CG PHE C 469 " ideal model delta sigma weight residual 113.80 119.86 -6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CB GLU B 47 " pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " ideal model delta sigma weight residual 112.60 121.85 -9.25 1.70e+00 3.46e-01 2.96e+01 ... (remaining 20979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 8104 15.25 - 30.49: 800 30.49 - 45.73: 188 45.73 - 60.98: 104 60.98 - 76.22: 48 Dihedral angle restraints: 9244 sinusoidal: 3644 harmonic: 5600 Sorted by residual: dihedral pdb=" CA PRO B 275 " pdb=" C PRO B 275 " pdb=" N CYS B 276 " pdb=" CA CYS B 276 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PRO A 275 " pdb=" C PRO A 275 " pdb=" N CYS A 276 " pdb=" CA CYS A 276 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA PRO D 275 " pdb=" C PRO D 275 " pdb=" N CYS D 276 " pdb=" CA CYS D 276 " ideal model delta harmonic sigma weight residual 180.00 153.80 26.20 0 5.00e+00 4.00e-02 2.75e+01 ... (remaining 9241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1048 0.050 - 0.101: 684 0.101 - 0.151: 440 0.151 - 0.202: 124 0.202 - 0.252: 28 Chirality restraints: 2324 Sorted by residual: chirality pdb=" CA ASN A 455 " pdb=" N ASN A 455 " pdb=" C ASN A 455 " pdb=" CB ASN A 455 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASN C 455 " pdb=" N ASN C 455 " pdb=" C ASN C 455 " pdb=" CB ASN C 455 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA ASN D 455 " pdb=" N ASN D 455 " pdb=" C ASN D 455 " pdb=" CB ASN D 455 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2321 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 265 " -0.233 9.50e-02 1.11e+02 1.07e-01 1.34e+01 pdb=" NE ARG D 265 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG D 265 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG D 265 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG D 265 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 265 " 0.233 9.50e-02 1.11e+02 1.07e-01 1.34e+01 pdb=" NE ARG C 265 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG C 265 " 0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG C 265 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG C 265 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 265 " -0.233 9.50e-02 1.11e+02 1.07e-01 1.34e+01 pdb=" NE ARG B 265 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 265 " -0.042 2.00e-02 2.50e+03 pdb=" NH1 ARG B 265 " 0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG B 265 " 0.006 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.44 - 2.93: 5636 2.93 - 3.42: 14702 3.42 - 3.91: 27146 3.91 - 4.41: 32122 4.41 - 4.90: 50950 Nonbonded interactions: 130556 Sorted by model distance: nonbonded pdb=" OD1 ASP C 438 " pdb=" N SER D 497 " model vdw 2.437 3.120 nonbonded pdb=" N SER C 497 " pdb=" OD1 ASP D 438 " model vdw 2.437 3.120 nonbonded pdb=" OD1 ASP A 438 " pdb=" N SER B 497 " model vdw 2.437 3.120 nonbonded pdb=" N SER A 497 " pdb=" OD1 ASP B 438 " model vdw 2.437 3.120 nonbonded pdb=" OE1 GLU C 312 " pdb=" OG SER C 314 " model vdw 2.528 3.040 ... (remaining 130551 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.380 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.010 0.056 15496 Z= 0.633 Angle : 1.695 9.248 20984 Z= 1.159 Chirality : 0.084 0.252 2324 Planarity : 0.010 0.107 2716 Dihedral : 15.363 76.218 5676 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 0.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.04 % Favored : 97.76 % Rotamer: Outliers : 1.49 % Allowed : 5.46 % Favored : 93.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 1964 helix: -0.91 (0.15), residues: 792 sheet: -0.01 (0.24), residues: 412 loop : -0.65 (0.20), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.007 ARG A 265 TYR 0.037 0.008 TYR B 481 PHE 0.038 0.008 PHE A 151 TRP 0.040 0.008 TRP A 178 HIS 0.012 0.004 HIS B 204 Details of bonding type rmsd covalent geometry : bond 0.00963 (15496) covalent geometry : angle 1.69471 (20984) hydrogen bonds : bond 0.19383 ( 720) hydrogen bonds : angle 7.19745 ( 2100) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 472 time to evaluate : 0.369 Fit side-chains REVERT: A 22 LYS cc_start: 0.6530 (mttt) cc_final: 0.6284 (mtmt) REVERT: A 31 ASP cc_start: 0.7135 (m-30) cc_final: 0.6585 (p0) REVERT: A 51 GLN cc_start: 0.6239 (mm110) cc_final: 0.5951 (mm-40) REVERT: A 53 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 57 LYS cc_start: 0.6739 (tttm) cc_final: 0.6534 (ttmt) REVERT: A 84 GLU cc_start: 0.6639 (tp30) cc_final: 0.5713 (mm-30) REVERT: A 97 GLU cc_start: 0.6025 (tt0) cc_final: 0.5621 (tt0) REVERT: A 109 MET cc_start: 0.7441 (ttm) cc_final: 0.7002 (mtm) REVERT: A 110 ASN cc_start: 0.7969 (t0) cc_final: 0.7716 (t0) REVERT: A 115 TYR cc_start: 0.7381 (t80) cc_final: 0.7157 (t80) REVERT: A 119 TYR cc_start: 0.7540 (t80) cc_final: 0.7118 (t80) REVERT: A 158 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6927 (tt0) REVERT: A 175 MET cc_start: 0.8095 (mmp) cc_final: 0.7870 (mmm) REVERT: A 238 ASP cc_start: 0.6962 (t70) cc_final: 0.6708 (t0) REVERT: A 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6758 (m-30) REVERT: A 245 THR cc_start: 0.7707 (m) cc_final: 0.7507 (p) REVERT: A 253 LEU cc_start: 0.7141 (mt) cc_final: 0.6899 (mm) REVERT: A 256 GLU cc_start: 0.6989 (tt0) cc_final: 0.6683 (tt0) REVERT: A 265 ARG cc_start: 0.7054 (mpt90) cc_final: 0.6752 (mmt-90) REVERT: A 293 HIS cc_start: 0.6754 (m-70) cc_final: 0.5122 (t-90) REVERT: A 315 ILE cc_start: 0.6976 (pt) cc_final: 0.6507 (pt) REVERT: A 321 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: A 329 LYS cc_start: 0.7457 (mttt) cc_final: 0.6991 (mtpm) REVERT: A 341 THR cc_start: 0.7461 (p) cc_final: 0.7228 (p) REVERT: A 356 ASP cc_start: 0.6114 (t70) cc_final: 0.5897 (t70) REVERT: A 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: A 364 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6142 (mt-10) REVERT: A 380 TYR cc_start: 0.6750 (m-80) cc_final: 0.5937 (m-80) REVERT: A 394 MET cc_start: 0.7472 (mtt) cc_final: 0.7108 (mtt) REVERT: A 399 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6901 (mt-10) REVERT: A 415 ASP cc_start: 0.6841 (m-30) cc_final: 0.6342 (p0) REVERT: A 416 ASP cc_start: 0.5713 (t70) cc_final: 0.5307 (t0) REVERT: A 423 ASN cc_start: 0.6753 (t0) cc_final: 0.6522 (t0) REVERT: A 425 PHE cc_start: 0.7674 (m-80) cc_final: 0.7382 (m-80) REVERT: A 436 ASP cc_start: 0.7104 (t70) cc_final: 0.6425 (t0) REVERT: A 477 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7079 (mm-30) REVERT: A 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7044 (tt0) REVERT: B 22 LYS cc_start: 0.6531 (mttt) cc_final: 0.6285 (mtmt) REVERT: B 31 ASP cc_start: 0.7131 (m-30) cc_final: 0.6594 (p0) REVERT: B 51 GLN cc_start: 0.6240 (mm110) cc_final: 0.5950 (mm-40) REVERT: B 53 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6974 (mm-30) REVERT: B 57 LYS cc_start: 0.6738 (tttm) cc_final: 0.6535 (ttmt) REVERT: B 84 GLU cc_start: 0.6638 (tp30) cc_final: 0.5713 (mm-30) REVERT: B 94 ASP cc_start: 0.7192 (m-30) cc_final: 0.6989 (m-30) REVERT: B 97 GLU cc_start: 0.6024 (tt0) cc_final: 0.5620 (tt0) REVERT: B 109 MET cc_start: 0.7440 (ttm) cc_final: 0.7002 (mtm) REVERT: B 110 ASN cc_start: 0.7966 (t0) cc_final: 0.7714 (t0) REVERT: B 115 TYR cc_start: 0.7382 (t80) cc_final: 0.7157 (t80) REVERT: B 119 TYR cc_start: 0.7540 (t80) cc_final: 0.7117 (t80) REVERT: B 158 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6925 (tt0) REVERT: B 175 MET cc_start: 0.8095 (mmp) cc_final: 0.7870 (mmm) REVERT: B 238 ASP cc_start: 0.6961 (t70) cc_final: 0.6707 (t0) REVERT: B 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6758 (m-30) REVERT: B 245 THR cc_start: 0.7707 (m) cc_final: 0.7507 (p) REVERT: B 253 LEU cc_start: 0.7141 (mt) cc_final: 0.6900 (mm) REVERT: B 256 GLU cc_start: 0.6987 (tt0) cc_final: 0.6682 (tt0) REVERT: B 265 ARG cc_start: 0.7055 (mpt90) cc_final: 0.6753 (mmt-90) REVERT: B 293 HIS cc_start: 0.6755 (m-70) cc_final: 0.5122 (t-90) REVERT: B 315 ILE cc_start: 0.6973 (pt) cc_final: 0.6505 (pt) REVERT: B 321 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7172 (ttp-110) REVERT: B 329 LYS cc_start: 0.7460 (mttt) cc_final: 0.6993 (mtpm) REVERT: B 341 THR cc_start: 0.7461 (p) cc_final: 0.7229 (p) REVERT: B 356 ASP cc_start: 0.6113 (t70) cc_final: 0.5896 (t70) REVERT: B 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: B 364 GLU cc_start: 0.6440 (mt-10) cc_final: 0.6146 (mt-10) REVERT: B 380 TYR cc_start: 0.6750 (m-80) cc_final: 0.5934 (m-80) REVERT: B 394 MET cc_start: 0.7474 (mtt) cc_final: 0.7109 (mtt) REVERT: B 399 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6900 (mt-10) REVERT: B 415 ASP cc_start: 0.6841 (m-30) cc_final: 0.6342 (p0) REVERT: B 416 ASP cc_start: 0.5713 (t70) cc_final: 0.5306 (t0) REVERT: B 423 ASN cc_start: 0.6752 (t0) cc_final: 0.6519 (t0) REVERT: B 425 PHE cc_start: 0.7673 (m-80) cc_final: 0.7382 (m-80) REVERT: B 436 ASP cc_start: 0.7105 (t70) cc_final: 0.6424 (t0) REVERT: B 477 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7080 (mm-30) REVERT: B 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7045 (tt0) REVERT: C 22 LYS cc_start: 0.6533 (mttt) cc_final: 0.6288 (mtmt) REVERT: C 31 ASP cc_start: 0.7136 (m-30) cc_final: 0.6596 (p0) REVERT: C 51 GLN cc_start: 0.6240 (mm110) cc_final: 0.5953 (mm-40) REVERT: C 53 GLU cc_start: 0.7900 (mm-30) cc_final: 0.6971 (mm-30) REVERT: C 57 LYS cc_start: 0.6736 (tttm) cc_final: 0.6532 (ttmt) REVERT: C 84 GLU cc_start: 0.6639 (tp30) cc_final: 0.5715 (mm-30) REVERT: C 97 GLU cc_start: 0.6025 (tt0) cc_final: 0.5621 (tt0) REVERT: C 109 MET cc_start: 0.7442 (ttm) cc_final: 0.7004 (mtm) REVERT: C 110 ASN cc_start: 0.7968 (t0) cc_final: 0.7715 (t0) REVERT: C 115 TYR cc_start: 0.7381 (t80) cc_final: 0.7157 (t80) REVERT: C 119 TYR cc_start: 0.7542 (t80) cc_final: 0.7119 (t80) REVERT: C 158 GLU cc_start: 0.7305 (mt-10) cc_final: 0.6924 (tt0) REVERT: C 175 MET cc_start: 0.8096 (mmp) cc_final: 0.7871 (mmm) REVERT: C 238 ASP cc_start: 0.6960 (t70) cc_final: 0.6702 (t0) REVERT: C 240 ASP cc_start: 0.7231 (m-30) cc_final: 0.6765 (m-30) REVERT: C 245 THR cc_start: 0.7708 (m) cc_final: 0.7507 (p) REVERT: C 253 LEU cc_start: 0.7142 (mt) cc_final: 0.6901 (mm) REVERT: C 256 GLU cc_start: 0.6987 (tt0) cc_final: 0.6682 (tt0) REVERT: C 265 ARG cc_start: 0.7054 (mpt90) cc_final: 0.6754 (mmt-90) REVERT: C 293 HIS cc_start: 0.6755 (m-70) cc_final: 0.5122 (t-90) REVERT: C 315 ILE cc_start: 0.6975 (pt) cc_final: 0.6505 (pt) REVERT: C 321 ARG cc_start: 0.7474 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: C 329 LYS cc_start: 0.7459 (mttt) cc_final: 0.6994 (mtpm) REVERT: C 341 THR cc_start: 0.7458 (p) cc_final: 0.7225 (p) REVERT: C 356 ASP cc_start: 0.6116 (t70) cc_final: 0.5898 (t70) REVERT: C 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6661 (mtpt) REVERT: C 364 GLU cc_start: 0.6441 (mt-10) cc_final: 0.6146 (mt-10) REVERT: C 380 TYR cc_start: 0.6749 (m-80) cc_final: 0.5948 (m-80) REVERT: C 394 MET cc_start: 0.7477 (mtt) cc_final: 0.7112 (mtt) REVERT: C 399 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6900 (mt-10) REVERT: C 415 ASP cc_start: 0.6840 (m-30) cc_final: 0.6342 (p0) REVERT: C 416 ASP cc_start: 0.5713 (t70) cc_final: 0.5307 (t0) REVERT: C 423 ASN cc_start: 0.6751 (t0) cc_final: 0.6518 (t0) REVERT: C 425 PHE cc_start: 0.7673 (m-80) cc_final: 0.7409 (m-80) REVERT: C 436 ASP cc_start: 0.7104 (t70) cc_final: 0.6426 (t0) REVERT: C 477 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7078 (mm-30) REVERT: C 480 GLU cc_start: 0.7684 (tt0) cc_final: 0.7044 (tt0) REVERT: D 22 LYS cc_start: 0.6531 (mttt) cc_final: 0.6286 (mtmt) REVERT: D 31 ASP cc_start: 0.7137 (m-30) cc_final: 0.6585 (p0) REVERT: D 51 GLN cc_start: 0.6239 (mm110) cc_final: 0.5951 (mm-40) REVERT: D 53 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7031 (mm-30) REVERT: D 57 LYS cc_start: 0.6738 (tttm) cc_final: 0.6533 (ttmt) REVERT: D 84 GLU cc_start: 0.6639 (tp30) cc_final: 0.5715 (mm-30) REVERT: D 94 ASP cc_start: 0.7192 (m-30) cc_final: 0.6990 (m-30) REVERT: D 97 GLU cc_start: 0.6023 (tt0) cc_final: 0.5621 (tt0) REVERT: D 109 MET cc_start: 0.7440 (ttm) cc_final: 0.7002 (mtm) REVERT: D 110 ASN cc_start: 0.7966 (t0) cc_final: 0.7714 (t0) REVERT: D 115 TYR cc_start: 0.7381 (t80) cc_final: 0.7157 (t80) REVERT: D 119 TYR cc_start: 0.7540 (t80) cc_final: 0.7118 (t80) REVERT: D 158 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6924 (tt0) REVERT: D 175 MET cc_start: 0.8095 (mmp) cc_final: 0.7871 (mmm) REVERT: D 238 ASP cc_start: 0.6961 (t70) cc_final: 0.6704 (t0) REVERT: D 240 ASP cc_start: 0.7229 (m-30) cc_final: 0.6764 (m-30) REVERT: D 245 THR cc_start: 0.7708 (m) cc_final: 0.7508 (p) REVERT: D 253 LEU cc_start: 0.7140 (mt) cc_final: 0.6899 (mm) REVERT: D 256 GLU cc_start: 0.6986 (tt0) cc_final: 0.6682 (tt0) REVERT: D 265 ARG cc_start: 0.7055 (mpt90) cc_final: 0.6753 (mmt-90) REVERT: D 293 HIS cc_start: 0.6756 (m-70) cc_final: 0.5122 (t-90) REVERT: D 315 ILE cc_start: 0.6974 (pt) cc_final: 0.6505 (pt) REVERT: D 321 ARG cc_start: 0.7475 (ttp80) cc_final: 0.7173 (ttp-110) REVERT: D 329 LYS cc_start: 0.7459 (mttt) cc_final: 0.6993 (mtpm) REVERT: D 341 THR cc_start: 0.7460 (p) cc_final: 0.7228 (p) REVERT: D 356 ASP cc_start: 0.6117 (t70) cc_final: 0.5899 (t70) REVERT: D 363 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6662 (mtpt) REVERT: D 364 GLU cc_start: 0.6439 (mt-10) cc_final: 0.6143 (mt-10) REVERT: D 380 TYR cc_start: 0.6749 (m-80) cc_final: 0.5948 (m-80) REVERT: D 394 MET cc_start: 0.7475 (mtt) cc_final: 0.7110 (mtt) REVERT: D 399 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6900 (mt-10) REVERT: D 415 ASP cc_start: 0.6840 (m-30) cc_final: 0.6340 (p0) REVERT: D 416 ASP cc_start: 0.5715 (t70) cc_final: 0.5308 (t0) REVERT: D 423 ASN cc_start: 0.6753 (t0) cc_final: 0.6520 (t0) REVERT: D 425 PHE cc_start: 0.7674 (m-80) cc_final: 0.7409 (m-80) REVERT: D 436 ASP cc_start: 0.7103 (t70) cc_final: 0.6424 (t0) REVERT: D 477 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7079 (mm-30) REVERT: D 480 GLU cc_start: 0.7682 (tt0) cc_final: 0.7044 (tt0) outliers start: 24 outliers final: 0 residues processed: 488 average time/residue: 0.5922 time to fit residues: 313.6791 Evaluate side-chains 286 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 282 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 363 LYS Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain C residue 363 LYS Chi-restraints excluded: chain D residue 363 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 383 GLN ** A 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN B 334 ASN B 383 GLN ** B 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 ASN C 334 ASN C 383 GLN ** C 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN D 334 ASN D 383 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.151933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.121726 restraints weight = 14712.754| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.37 r_work: 0.3172 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15496 Z= 0.142 Angle : 0.575 6.763 20984 Z= 0.313 Chirality : 0.046 0.224 2324 Planarity : 0.004 0.035 2716 Dihedral : 5.255 18.958 2120 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.42 % Allowed : 14.33 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.18), residues: 1964 helix: 0.93 (0.17), residues: 824 sheet: 0.43 (0.24), residues: 412 loop : 0.14 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 85 TYR 0.015 0.002 TYR C 20 PHE 0.010 0.002 PHE C 38 TRP 0.008 0.001 TRP C 178 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00314 (15496) covalent geometry : angle 0.57543 (20984) hydrogen bonds : bond 0.04049 ( 720) hydrogen bonds : angle 5.38187 ( 2100) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 318 time to evaluate : 0.453 Fit side-chains REVERT: A 31 ASP cc_start: 0.7409 (m-30) cc_final: 0.7111 (p0) REVERT: A 53 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7807 (mm-30) REVERT: A 57 LYS cc_start: 0.7853 (tttm) cc_final: 0.7480 (tttp) REVERT: A 84 GLU cc_start: 0.7524 (tp30) cc_final: 0.7023 (mm-30) REVERT: A 98 ARG cc_start: 0.7963 (ttp-170) cc_final: 0.7633 (ttp-170) REVERT: A 107 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6255 (tp30) REVERT: A 119 TYR cc_start: 0.8304 (t80) cc_final: 0.7899 (t80) REVERT: A 127 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8549 (mp) REVERT: A 158 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7246 (tt0) REVERT: A 193 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8066 (tmmt) REVERT: A 240 ASP cc_start: 0.7973 (m-30) cc_final: 0.7677 (m-30) REVERT: A 253 LEU cc_start: 0.8153 (mt) cc_final: 0.7851 (mm) REVERT: A 285 ASP cc_start: 0.7198 (t0) cc_final: 0.6934 (p0) REVERT: A 293 HIS cc_start: 0.7513 (m-70) cc_final: 0.6359 (t-90) REVERT: A 295 VAL cc_start: 0.8228 (p) cc_final: 0.7766 (t) REVERT: A 325 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7625 (tp30) REVERT: A 329 LYS cc_start: 0.7689 (mttt) cc_final: 0.7276 (mtpm) REVERT: A 352 ASP cc_start: 0.7747 (m-30) cc_final: 0.7361 (m-30) REVERT: A 357 LEU cc_start: 0.7365 (mt) cc_final: 0.6772 (mt) REVERT: A 367 LYS cc_start: 0.8346 (tttt) cc_final: 0.7941 (tttm) REVERT: A 380 TYR cc_start: 0.7514 (m-80) cc_final: 0.6932 (m-80) REVERT: A 416 ASP cc_start: 0.6563 (t70) cc_final: 0.6254 (t0) REVERT: A 442 THR cc_start: 0.8455 (m) cc_final: 0.8152 (m) REVERT: B 31 ASP cc_start: 0.7414 (m-30) cc_final: 0.7111 (p0) REVERT: B 53 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7800 (mm-30) REVERT: B 57 LYS cc_start: 0.7846 (tttm) cc_final: 0.7474 (tttp) REVERT: B 84 GLU cc_start: 0.7537 (tp30) cc_final: 0.7023 (mm-30) REVERT: B 98 ARG cc_start: 0.7961 (ttp-170) cc_final: 0.7638 (ttp-170) REVERT: B 107 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6254 (tp30) REVERT: B 119 TYR cc_start: 0.8296 (t80) cc_final: 0.7894 (t80) REVERT: B 127 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8541 (mp) REVERT: B 158 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7258 (tt0) REVERT: B 193 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8066 (tmmt) REVERT: B 240 ASP cc_start: 0.7968 (m-30) cc_final: 0.7673 (m-30) REVERT: B 253 LEU cc_start: 0.8162 (mt) cc_final: 0.7864 (mm) REVERT: B 285 ASP cc_start: 0.7199 (t0) cc_final: 0.6935 (p0) REVERT: B 293 HIS cc_start: 0.7502 (m-70) cc_final: 0.6348 (t-90) REVERT: B 295 VAL cc_start: 0.8221 (p) cc_final: 0.7760 (t) REVERT: B 325 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7621 (tp30) REVERT: B 329 LYS cc_start: 0.7686 (mttt) cc_final: 0.7266 (mtpm) REVERT: B 352 ASP cc_start: 0.7740 (m-30) cc_final: 0.7350 (m-30) REVERT: B 357 LEU cc_start: 0.7354 (mt) cc_final: 0.6761 (mt) REVERT: B 367 LYS cc_start: 0.8340 (tttt) cc_final: 0.7933 (tttm) REVERT: B 380 TYR cc_start: 0.7516 (m-80) cc_final: 0.6938 (m-80) REVERT: B 416 ASP cc_start: 0.6540 (t70) cc_final: 0.6237 (t0) REVERT: B 442 THR cc_start: 0.8456 (m) cc_final: 0.8147 (m) REVERT: C 31 ASP cc_start: 0.7425 (m-30) cc_final: 0.7120 (p0) REVERT: C 53 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7807 (mm-30) REVERT: C 57 LYS cc_start: 0.7845 (tttm) cc_final: 0.7478 (tttp) REVERT: C 84 GLU cc_start: 0.7558 (tp30) cc_final: 0.7027 (mm-30) REVERT: C 98 ARG cc_start: 0.7948 (ttp-170) cc_final: 0.7617 (ttp-170) REVERT: C 107 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6251 (tp30) REVERT: C 119 TYR cc_start: 0.8299 (t80) cc_final: 0.7891 (t80) REVERT: C 127 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8538 (mp) REVERT: C 158 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7242 (tt0) REVERT: C 240 ASP cc_start: 0.7979 (m-30) cc_final: 0.7632 (m-30) REVERT: C 253 LEU cc_start: 0.8164 (mt) cc_final: 0.7863 (mm) REVERT: C 285 ASP cc_start: 0.7207 (t0) cc_final: 0.6937 (p0) REVERT: C 293 HIS cc_start: 0.7512 (m-70) cc_final: 0.6353 (t-90) REVERT: C 295 VAL cc_start: 0.8244 (p) cc_final: 0.7781 (t) REVERT: C 325 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7613 (tp30) REVERT: C 329 LYS cc_start: 0.7678 (mttt) cc_final: 0.7265 (mtpm) REVERT: C 352 ASP cc_start: 0.7753 (m-30) cc_final: 0.7365 (m-30) REVERT: C 357 LEU cc_start: 0.7349 (mt) cc_final: 0.6760 (mt) REVERT: C 367 LYS cc_start: 0.8345 (tttt) cc_final: 0.7938 (tttm) REVERT: C 380 TYR cc_start: 0.7519 (m-80) cc_final: 0.6918 (m-80) REVERT: C 416 ASP cc_start: 0.6598 (t70) cc_final: 0.6292 (t0) REVERT: C 442 THR cc_start: 0.8458 (m) cc_final: 0.8156 (m) REVERT: D 31 ASP cc_start: 0.7435 (m-30) cc_final: 0.7113 (p0) REVERT: D 53 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7802 (mm-30) REVERT: D 57 LYS cc_start: 0.7840 (tttm) cc_final: 0.7470 (tttp) REVERT: D 84 GLU cc_start: 0.7581 (tp30) cc_final: 0.7040 (mm-30) REVERT: D 98 ARG cc_start: 0.7962 (ttp-170) cc_final: 0.7638 (ttp-170) REVERT: D 107 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6252 (tp30) REVERT: D 119 TYR cc_start: 0.8293 (t80) cc_final: 0.7889 (t80) REVERT: D 127 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8541 (mp) REVERT: D 158 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7242 (tt0) REVERT: D 193 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8058 (tmmt) REVERT: D 240 ASP cc_start: 0.7968 (m-30) cc_final: 0.7629 (m-30) REVERT: D 253 LEU cc_start: 0.8157 (mt) cc_final: 0.7860 (mm) REVERT: D 285 ASP cc_start: 0.7223 (t0) cc_final: 0.6939 (p0) REVERT: D 293 HIS cc_start: 0.7490 (m-70) cc_final: 0.6353 (t-90) REVERT: D 295 VAL cc_start: 0.8230 (p) cc_final: 0.7769 (t) REVERT: D 325 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7621 (tp30) REVERT: D 329 LYS cc_start: 0.7683 (mttt) cc_final: 0.7270 (mtpm) REVERT: D 352 ASP cc_start: 0.7735 (m-30) cc_final: 0.7343 (m-30) REVERT: D 357 LEU cc_start: 0.7343 (mt) cc_final: 0.6756 (mt) REVERT: D 367 LYS cc_start: 0.8340 (tttt) cc_final: 0.7936 (tttm) REVERT: D 380 TYR cc_start: 0.7510 (m-80) cc_final: 0.6913 (m-80) REVERT: D 416 ASP cc_start: 0.6577 (t70) cc_final: 0.6264 (t0) REVERT: D 442 THR cc_start: 0.8455 (m) cc_final: 0.8143 (m) outliers start: 39 outliers final: 4 residues processed: 353 average time/residue: 0.5358 time to fit residues: 207.8771 Evaluate side-chains 271 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 256 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 127 ILE Chi-restraints excluded: chain D residue 193 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 121 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 186 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 GLN A 500 ASN B 463 GLN B 500 ASN C 463 GLN C 500 ASN D 463 GLN D 500 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.146901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.117991 restraints weight = 15132.659| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.33 r_work: 0.3155 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15496 Z= 0.178 Angle : 0.567 7.043 20984 Z= 0.304 Chirality : 0.047 0.164 2324 Planarity : 0.004 0.030 2716 Dihedral : 4.996 22.084 2104 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.85 % Allowed : 16.38 % Favored : 80.77 % 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 aren not related in a simple way. whole: 0.95 (0.19), residues: 1964 helix: 1.19 (0.17), residues: 828 sheet: 0.34 (0.26), residues: 408 loop : 0.33 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 321 TYR 0.014 0.002 TYR C 154 PHE 0.013 0.002 PHE D 171 TRP 0.010 0.002 TRP C 178 HIS 0.006 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00423 (15496) covalent geometry : angle 0.56658 (20984) hydrogen bonds : bond 0.04163 ( 720) hydrogen bonds : angle 5.21405 ( 2100) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 284 time to evaluate : 0.570 Fit side-chains REVERT: A 31 ASP cc_start: 0.7393 (m-30) cc_final: 0.7038 (p0) REVERT: A 53 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 57 LYS cc_start: 0.7796 (tttm) cc_final: 0.7201 (ttmt) REVERT: A 69 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7839 (tm-30) REVERT: A 84 GLU cc_start: 0.7425 (tp30) cc_final: 0.6921 (mm-30) REVERT: A 98 ARG cc_start: 0.7987 (ttp-170) cc_final: 0.7663 (ttp-170) REVERT: A 107 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: A 117 ASN cc_start: 0.8110 (m-40) cc_final: 0.7749 (m-40) REVERT: A 119 TYR cc_start: 0.8325 (t80) cc_final: 0.8016 (t80) REVERT: A 240 ASP cc_start: 0.7875 (m-30) cc_final: 0.7570 (m-30) REVERT: A 269 GLU cc_start: 0.7144 (tp30) cc_final: 0.6680 (tt0) REVERT: A 293 HIS cc_start: 0.7468 (m-70) cc_final: 0.6371 (t-90) REVERT: A 321 ARG cc_start: 0.7632 (ttp80) cc_final: 0.7430 (ttp-110) REVERT: A 325 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7465 (tp30) REVERT: A 329 LYS cc_start: 0.7808 (mttt) cc_final: 0.7307 (mtpm) REVERT: A 352 ASP cc_start: 0.7876 (m-30) cc_final: 0.7463 (m-30) REVERT: A 353 LYS cc_start: 0.6789 (ttpp) cc_final: 0.6451 (tptt) REVERT: A 357 LEU cc_start: 0.7280 (mt) cc_final: 0.6814 (mt) REVERT: A 367 LYS cc_start: 0.8313 (tttt) cc_final: 0.7910 (tttm) REVERT: A 380 TYR cc_start: 0.7597 (m-80) cc_final: 0.7058 (m-80) REVERT: A 409 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7420 (mtt) REVERT: A 477 GLU cc_start: 0.8460 (mt-10) cc_final: 0.7963 (mt-10) REVERT: B 31 ASP cc_start: 0.7369 (m-30) cc_final: 0.7023 (p0) REVERT: B 53 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7850 (mm-30) REVERT: B 57 LYS cc_start: 0.7802 (tttm) cc_final: 0.7212 (ttmt) REVERT: B 69 GLN cc_start: 0.8081 (tp-100) cc_final: 0.7824 (tm-30) REVERT: B 84 GLU cc_start: 0.7379 (tp30) cc_final: 0.6891 (mm-30) REVERT: B 98 ARG cc_start: 0.7995 (ttp-170) cc_final: 0.7666 (ttp-170) REVERT: B 107 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: B 117 ASN cc_start: 0.8115 (m-40) cc_final: 0.7747 (m-40) REVERT: B 119 TYR cc_start: 0.8305 (t80) cc_final: 0.7995 (t80) REVERT: B 240 ASP cc_start: 0.7882 (m-30) cc_final: 0.7581 (m-30) REVERT: B 269 GLU cc_start: 0.7121 (tp30) cc_final: 0.6666 (tt0) REVERT: B 293 HIS cc_start: 0.7462 (m-70) cc_final: 0.6367 (t-90) REVERT: B 325 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7465 (tp30) REVERT: B 329 LYS cc_start: 0.7796 (mttt) cc_final: 0.7294 (mtpm) REVERT: B 352 ASP cc_start: 0.7887 (m-30) cc_final: 0.7476 (m-30) REVERT: B 353 LYS cc_start: 0.6810 (ttpp) cc_final: 0.6473 (tptt) REVERT: B 357 LEU cc_start: 0.7297 (mt) cc_final: 0.6830 (mt) REVERT: B 367 LYS cc_start: 0.8315 (tttt) cc_final: 0.7911 (tttm) REVERT: B 380 TYR cc_start: 0.7592 (m-80) cc_final: 0.7054 (m-80) REVERT: B 409 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7424 (mtt) REVERT: B 477 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7977 (mt-10) REVERT: C 31 ASP cc_start: 0.7395 (m-30) cc_final: 0.7037 (p0) REVERT: C 53 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7847 (mm-30) REVERT: C 57 LYS cc_start: 0.7801 (tttm) cc_final: 0.7215 (ttmt) REVERT: C 69 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7829 (tm-30) REVERT: C 84 GLU cc_start: 0.7404 (tp30) cc_final: 0.6914 (mm-30) REVERT: C 98 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7654 (ttp-170) REVERT: C 107 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6311 (tp30) REVERT: C 117 ASN cc_start: 0.8112 (m-40) cc_final: 0.7748 (m-40) REVERT: C 240 ASP cc_start: 0.7861 (m-30) cc_final: 0.7567 (m-30) REVERT: C 269 GLU cc_start: 0.7160 (tp30) cc_final: 0.6691 (tt0) REVERT: C 293 HIS cc_start: 0.7469 (m-70) cc_final: 0.6359 (t-90) REVERT: C 321 ARG cc_start: 0.7633 (ttp80) cc_final: 0.7431 (ttp-110) REVERT: C 325 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7485 (tp30) REVERT: C 329 LYS cc_start: 0.7801 (mttt) cc_final: 0.7295 (mtpm) REVERT: C 352 ASP cc_start: 0.7880 (m-30) cc_final: 0.7489 (m-30) REVERT: C 353 LYS cc_start: 0.6797 (ttpp) cc_final: 0.6457 (tptt) REVERT: C 357 LEU cc_start: 0.7286 (mt) cc_final: 0.6821 (mt) REVERT: C 367 LYS cc_start: 0.8324 (tttt) cc_final: 0.7924 (tttm) REVERT: C 380 TYR cc_start: 0.7606 (m-80) cc_final: 0.7117 (m-80) REVERT: C 409 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7415 (mtt) REVERT: C 477 GLU cc_start: 0.8483 (mt-10) cc_final: 0.7994 (mt-10) REVERT: D 31 ASP cc_start: 0.7381 (m-30) cc_final: 0.7022 (p0) REVERT: D 53 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7843 (mm-30) REVERT: D 57 LYS cc_start: 0.7797 (tttm) cc_final: 0.7210 (ttmt) REVERT: D 69 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7833 (tm-30) REVERT: D 84 GLU cc_start: 0.7394 (tp30) cc_final: 0.6907 (mm-30) REVERT: D 98 ARG cc_start: 0.7985 (ttp-170) cc_final: 0.7660 (ttp-170) REVERT: D 107 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6296 (tp30) REVERT: D 117 ASN cc_start: 0.8117 (m-40) cc_final: 0.7755 (m-40) REVERT: D 240 ASP cc_start: 0.7862 (m-30) cc_final: 0.7562 (m-30) REVERT: D 269 GLU cc_start: 0.7164 (tp30) cc_final: 0.6697 (tt0) REVERT: D 293 HIS cc_start: 0.7463 (m-70) cc_final: 0.6349 (t-90) REVERT: D 321 ARG cc_start: 0.7637 (ttp80) cc_final: 0.7431 (ttp-110) REVERT: D 325 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7463 (tp30) REVERT: D 329 LYS cc_start: 0.7796 (mttt) cc_final: 0.7292 (mtpm) REVERT: D 352 ASP cc_start: 0.7882 (m-30) cc_final: 0.7496 (m-30) REVERT: D 353 LYS cc_start: 0.6803 (ttpp) cc_final: 0.6463 (tptt) REVERT: D 357 LEU cc_start: 0.7289 (mt) cc_final: 0.6827 (mt) REVERT: D 367 LYS cc_start: 0.8307 (tttt) cc_final: 0.7902 (tttm) REVERT: D 380 TYR cc_start: 0.7601 (m-80) cc_final: 0.7112 (m-80) REVERT: D 409 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7417 (mtt) REVERT: D 477 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7995 (mt-10) outliers start: 46 outliers final: 8 residues processed: 318 average time/residue: 0.5264 time to fit residues: 184.9166 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 3 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN B 72 GLN C 72 GLN D 72 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117295 restraints weight = 15297.338| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.37 r_work: 0.3154 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15496 Z= 0.129 Angle : 0.505 6.637 20984 Z= 0.271 Chirality : 0.044 0.142 2324 Planarity : 0.004 0.036 2716 Dihedral : 4.785 20.405 2104 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.61 % Allowed : 19.91 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.19), residues: 1964 helix: 1.72 (0.18), residues: 796 sheet: 0.25 (0.25), residues: 420 loop : 0.16 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 321 TYR 0.015 0.002 TYR A 20 PHE 0.007 0.001 PHE D 296 TRP 0.007 0.001 TRP C 178 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd covalent geometry : bond 0.00300 (15496) covalent geometry : angle 0.50478 (20984) hydrogen bonds : bond 0.03494 ( 720) hydrogen bonds : angle 5.05021 ( 2100) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 0.670 Fit side-chains REVERT: A 31 ASP cc_start: 0.7432 (m-30) cc_final: 0.7021 (p0) REVERT: A 53 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 57 LYS cc_start: 0.7724 (tttm) cc_final: 0.7275 (tttp) REVERT: A 69 GLN cc_start: 0.8047 (tp-100) cc_final: 0.7791 (tm-30) REVERT: A 84 GLU cc_start: 0.7364 (tp30) cc_final: 0.6936 (mm-30) REVERT: A 98 ARG cc_start: 0.8035 (ttp-170) cc_final: 0.7722 (ttp-170) REVERT: A 107 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: A 117 ASN cc_start: 0.8131 (m-40) cc_final: 0.7720 (m-40) REVERT: A 193 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7723 (tmmt) REVERT: A 240 ASP cc_start: 0.7874 (m-30) cc_final: 0.7581 (m-30) REVERT: A 293 HIS cc_start: 0.7484 (m-70) cc_final: 0.6342 (t-90) REVERT: A 313 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: A 325 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7474 (tp30) REVERT: A 329 LYS cc_start: 0.7709 (mttt) cc_final: 0.7326 (mtpm) REVERT: A 352 ASP cc_start: 0.7887 (m-30) cc_final: 0.7506 (m-30) REVERT: A 353 LYS cc_start: 0.6809 (ttpp) cc_final: 0.6498 (tptp) REVERT: A 357 LEU cc_start: 0.7307 (mt) cc_final: 0.6844 (mt) REVERT: A 367 LYS cc_start: 0.8319 (tttt) cc_final: 0.7931 (tttm) REVERT: A 380 TYR cc_start: 0.7612 (m-80) cc_final: 0.7071 (m-80) REVERT: A 412 LYS cc_start: 0.7624 (mtmt) cc_final: 0.7351 (mtpt) REVERT: A 416 ASP cc_start: 0.7345 (m-30) cc_final: 0.6875 (t0) REVERT: B 31 ASP cc_start: 0.7460 (m-30) cc_final: 0.7033 (p0) REVERT: B 53 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 57 LYS cc_start: 0.7733 (tttm) cc_final: 0.7294 (tttp) REVERT: B 69 GLN cc_start: 0.8037 (tp-100) cc_final: 0.7780 (tm-30) REVERT: B 84 GLU cc_start: 0.7356 (tp30) cc_final: 0.6912 (mm-30) REVERT: B 98 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7724 (ttp-170) REVERT: B 107 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.6391 (tp30) REVERT: B 117 ASN cc_start: 0.8138 (m-40) cc_final: 0.7730 (m-40) REVERT: B 193 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7727 (tmmt) REVERT: B 240 ASP cc_start: 0.7886 (m-30) cc_final: 0.7595 (m-30) REVERT: B 293 HIS cc_start: 0.7464 (m-70) cc_final: 0.6319 (t-90) REVERT: B 313 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6537 (pm20) REVERT: B 325 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7522 (tp30) REVERT: B 329 LYS cc_start: 0.7705 (mttt) cc_final: 0.7318 (mtpm) REVERT: B 352 ASP cc_start: 0.7881 (m-30) cc_final: 0.7497 (m-30) REVERT: B 353 LYS cc_start: 0.6812 (ttpp) cc_final: 0.6492 (tptp) REVERT: B 357 LEU cc_start: 0.7298 (mt) cc_final: 0.6837 (mt) REVERT: B 367 LYS cc_start: 0.8323 (tttt) cc_final: 0.7940 (tttm) REVERT: B 380 TYR cc_start: 0.7611 (m-80) cc_final: 0.7072 (m-80) REVERT: B 412 LYS cc_start: 0.7607 (mtmt) cc_final: 0.7377 (mtpt) REVERT: C 31 ASP cc_start: 0.7450 (m-30) cc_final: 0.7027 (p0) REVERT: C 53 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7735 (mm-30) REVERT: C 57 LYS cc_start: 0.7728 (tttm) cc_final: 0.7289 (tttp) REVERT: C 69 GLN cc_start: 0.8049 (tp-100) cc_final: 0.7792 (tm-30) REVERT: C 84 GLU cc_start: 0.7362 (tp30) cc_final: 0.6928 (mm-30) REVERT: C 98 ARG cc_start: 0.8007 (ttp-170) cc_final: 0.7689 (ttp-170) REVERT: C 107 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6329 (tp30) REVERT: C 117 ASN cc_start: 0.8131 (m-40) cc_final: 0.7719 (m-40) REVERT: C 240 ASP cc_start: 0.7887 (m-30) cc_final: 0.7600 (m-30) REVERT: C 293 HIS cc_start: 0.7470 (m-70) cc_final: 0.6336 (t-90) REVERT: C 325 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7480 (tp30) REVERT: C 329 LYS cc_start: 0.7697 (mttt) cc_final: 0.7311 (mtpm) REVERT: C 352 ASP cc_start: 0.7860 (m-30) cc_final: 0.7475 (m-30) REVERT: C 353 LYS cc_start: 0.6733 (ttpp) cc_final: 0.6409 (tptp) REVERT: C 357 LEU cc_start: 0.7309 (mt) cc_final: 0.6847 (mt) REVERT: C 367 LYS cc_start: 0.8319 (tttt) cc_final: 0.7933 (tttm) REVERT: C 380 TYR cc_start: 0.7621 (m-80) cc_final: 0.7065 (m-80) REVERT: D 31 ASP cc_start: 0.7437 (m-30) cc_final: 0.7021 (p0) REVERT: D 53 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7723 (mm-30) REVERT: D 57 LYS cc_start: 0.7726 (tttm) cc_final: 0.7288 (tttp) REVERT: D 69 GLN cc_start: 0.8036 (tp-100) cc_final: 0.7782 (tm-30) REVERT: D 84 GLU cc_start: 0.7375 (tp30) cc_final: 0.6928 (mm-30) REVERT: D 98 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7686 (ttp-170) REVERT: D 107 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6350 (tp30) REVERT: D 117 ASN cc_start: 0.8119 (m-40) cc_final: 0.7706 (m-40) REVERT: D 193 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7730 (tmmt) REVERT: D 240 ASP cc_start: 0.7867 (m-30) cc_final: 0.7580 (m-30) REVERT: D 293 HIS cc_start: 0.7449 (m-70) cc_final: 0.6297 (t-90) REVERT: D 325 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7496 (tp30) REVERT: D 329 LYS cc_start: 0.7706 (mttt) cc_final: 0.7331 (mtpm) REVERT: D 352 ASP cc_start: 0.7873 (m-30) cc_final: 0.7490 (m-30) REVERT: D 353 LYS cc_start: 0.6748 (ttpp) cc_final: 0.6426 (tptp) REVERT: D 357 LEU cc_start: 0.7313 (mt) cc_final: 0.6854 (mt) REVERT: D 367 LYS cc_start: 0.8318 (tttt) cc_final: 0.7932 (tttm) REVERT: D 380 TYR cc_start: 0.7600 (m-80) cc_final: 0.7045 (m-80) outliers start: 42 outliers final: 12 residues processed: 305 average time/residue: 0.5412 time to fit residues: 181.9332 Evaluate side-chains 273 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 193 LYS Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 193 LYS Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 118 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.113663 restraints weight = 15459.278| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.35 r_work: 0.3134 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 15496 Z= 0.316 Angle : 0.671 7.695 20984 Z= 0.358 Chirality : 0.051 0.318 2324 Planarity : 0.005 0.039 2716 Dihedral : 5.292 23.356 2104 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.47 % Allowed : 18.49 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 1964 helix: 1.05 (0.18), residues: 808 sheet: 0.13 (0.26), residues: 408 loop : 0.01 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 326 TYR 0.022 0.003 TYR A 351 PHE 0.017 0.003 PHE D 483 TRP 0.011 0.002 TRP A 136 HIS 0.005 0.002 HIS D 236 Details of bonding type rmsd covalent geometry : bond 0.00766 (15496) covalent geometry : angle 0.67070 (20984) hydrogen bonds : bond 0.04828 ( 720) hydrogen bonds : angle 5.48156 ( 2100) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.605 Fit side-chains REVERT: A 31 ASP cc_start: 0.7413 (m-30) cc_final: 0.7043 (p0) REVERT: A 53 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7539 (mm-30) REVERT: A 57 LYS cc_start: 0.7796 (tttm) cc_final: 0.7486 (tttp) REVERT: A 84 GLU cc_start: 0.7542 (tp30) cc_final: 0.7182 (mp0) REVERT: A 107 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.5714 (mm-30) REVERT: A 240 ASP cc_start: 0.7948 (m-30) cc_final: 0.7599 (m-30) REVERT: A 293 HIS cc_start: 0.7528 (m-70) cc_final: 0.6318 (t70) REVERT: A 325 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7515 (tp30) REVERT: A 329 LYS cc_start: 0.7612 (mttt) cc_final: 0.7197 (mtpm) REVERT: A 352 ASP cc_start: 0.7905 (m-30) cc_final: 0.7526 (m-30) REVERT: A 353 LYS cc_start: 0.6854 (ttpp) cc_final: 0.6464 (tptp) REVERT: A 357 LEU cc_start: 0.7383 (mt) cc_final: 0.6929 (mt) REVERT: A 367 LYS cc_start: 0.8408 (tttt) cc_final: 0.8025 (tttm) REVERT: A 380 TYR cc_start: 0.7592 (m-80) cc_final: 0.7151 (m-80) REVERT: A 409 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7288 (mtm) REVERT: A 412 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7408 (mtpt) REVERT: A 435 LYS cc_start: 0.7694 (mttm) cc_final: 0.7460 (mttm) REVERT: B 31 ASP cc_start: 0.7402 (m-30) cc_final: 0.7037 (p0) REVERT: B 53 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7555 (mm-30) REVERT: B 57 LYS cc_start: 0.7800 (tttm) cc_final: 0.7492 (tttp) REVERT: B 84 GLU cc_start: 0.7507 (tp30) cc_final: 0.7180 (mp0) REVERT: B 107 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.5747 (mm-30) REVERT: B 240 ASP cc_start: 0.7965 (m-30) cc_final: 0.7617 (m-30) REVERT: B 293 HIS cc_start: 0.7521 (m-70) cc_final: 0.6297 (t70) REVERT: B 313 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: B 325 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7554 (tp30) REVERT: B 329 LYS cc_start: 0.7606 (mttt) cc_final: 0.7193 (mtpm) REVERT: B 352 ASP cc_start: 0.7910 (m-30) cc_final: 0.7528 (m-30) REVERT: B 353 LYS cc_start: 0.6888 (ttpp) cc_final: 0.6493 (tptp) REVERT: B 357 LEU cc_start: 0.7395 (mt) cc_final: 0.6944 (mt) REVERT: B 367 LYS cc_start: 0.8419 (tttt) cc_final: 0.8040 (tttm) REVERT: B 380 TYR cc_start: 0.7605 (m-80) cc_final: 0.7172 (m-80) REVERT: B 409 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7267 (mtm) REVERT: B 412 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7407 (mtpt) REVERT: B 416 ASP cc_start: 0.7685 (OUTLIER) cc_final: 0.7051 (m-30) REVERT: B 435 LYS cc_start: 0.7694 (mttm) cc_final: 0.7464 (mttm) REVERT: C 31 ASP cc_start: 0.7392 (m-30) cc_final: 0.7036 (p0) REVERT: C 53 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7549 (mm-30) REVERT: C 57 LYS cc_start: 0.7795 (tttm) cc_final: 0.7487 (tttp) REVERT: C 84 GLU cc_start: 0.7546 (tp30) cc_final: 0.7178 (mp0) REVERT: C 107 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5719 (mm-30) REVERT: C 240 ASP cc_start: 0.7940 (m-30) cc_final: 0.7600 (m-30) REVERT: C 293 HIS cc_start: 0.7520 (m-70) cc_final: 0.6321 (t70) REVERT: C 325 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7552 (tp30) REVERT: C 329 LYS cc_start: 0.7593 (mttt) cc_final: 0.7180 (mtpm) REVERT: C 352 ASP cc_start: 0.7870 (m-30) cc_final: 0.7456 (m-30) REVERT: C 353 LYS cc_start: 0.6867 (ttpp) cc_final: 0.6468 (tptp) REVERT: C 357 LEU cc_start: 0.7388 (mt) cc_final: 0.6932 (mt) REVERT: C 367 LYS cc_start: 0.8415 (tttt) cc_final: 0.8040 (tttm) REVERT: C 380 TYR cc_start: 0.7608 (m-80) cc_final: 0.7167 (m-80) REVERT: C 409 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7359 (mtt) REVERT: C 435 LYS cc_start: 0.7687 (mttm) cc_final: 0.7456 (mttm) REVERT: D 31 ASP cc_start: 0.7400 (m-30) cc_final: 0.7035 (p0) REVERT: D 53 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7540 (mm-30) REVERT: D 57 LYS cc_start: 0.7793 (tttm) cc_final: 0.7484 (tttp) REVERT: D 84 GLU cc_start: 0.7512 (tp30) cc_final: 0.7188 (mp0) REVERT: D 107 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.5727 (mm-30) REVERT: D 240 ASP cc_start: 0.7935 (m-30) cc_final: 0.7596 (m-30) REVERT: D 293 HIS cc_start: 0.7521 (m-70) cc_final: 0.6316 (t70) REVERT: D 325 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7543 (tp30) REVERT: D 329 LYS cc_start: 0.7615 (mttt) cc_final: 0.7206 (mtpm) REVERT: D 352 ASP cc_start: 0.7892 (m-30) cc_final: 0.7481 (m-30) REVERT: D 353 LYS cc_start: 0.6864 (ttpp) cc_final: 0.6473 (tptp) REVERT: D 357 LEU cc_start: 0.7400 (mt) cc_final: 0.6946 (mt) REVERT: D 367 LYS cc_start: 0.8420 (tttt) cc_final: 0.8044 (tttm) REVERT: D 380 TYR cc_start: 0.7611 (m-80) cc_final: 0.7174 (m-80) REVERT: D 409 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7279 (mtm) REVERT: D 416 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7044 (m-30) REVERT: D 435 LYS cc_start: 0.7694 (mttm) cc_final: 0.7464 (mttm) outliers start: 56 outliers final: 12 residues processed: 298 average time/residue: 0.5853 time to fit residues: 191.8770 Evaluate side-chains 263 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 240 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 163 optimal weight: 0.8980 chunk 3 optimal weight: 0.0470 chunk 124 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 25 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 143 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 117 ASN A 121 ASN A 220 ASN B 19 GLN B 117 ASN B 121 ASN B 220 ASN C 19 GLN C 117 ASN C 121 ASN C 220 ASN D 19 GLN D 117 ASN D 121 ASN D 220 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.145669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117561 restraints weight = 15420.584| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.37 r_work: 0.3172 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15496 Z= 0.123 Angle : 0.509 6.715 20984 Z= 0.271 Chirality : 0.045 0.311 2324 Planarity : 0.004 0.030 2716 Dihedral : 4.805 20.458 2104 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.16 % Allowed : 20.60 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1964 helix: 1.59 (0.18), residues: 804 sheet: 0.14 (0.28), residues: 352 loop : 0.10 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.018 0.002 TYR B 351 PHE 0.007 0.001 PHE C 310 TRP 0.008 0.001 TRP A 453 HIS 0.003 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00281 (15496) covalent geometry : angle 0.50854 (20984) hydrogen bonds : bond 0.03437 ( 720) hydrogen bonds : angle 5.11463 ( 2100) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 279 time to evaluate : 0.469 Fit side-chains REVERT: A 31 ASP cc_start: 0.7431 (m-30) cc_final: 0.7031 (p0) REVERT: A 53 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7608 (mm-30) REVERT: A 57 LYS cc_start: 0.7664 (tttm) cc_final: 0.7204 (ttmt) REVERT: A 84 GLU cc_start: 0.7425 (tp30) cc_final: 0.7008 (mm-30) REVERT: A 90 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: A 107 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6312 (tp30) REVERT: A 220 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8674 (m-40) REVERT: A 240 ASP cc_start: 0.7966 (m-30) cc_final: 0.7562 (m-30) REVERT: A 293 HIS cc_start: 0.7437 (m-70) cc_final: 0.6281 (t-90) REVERT: A 325 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7575 (tp30) REVERT: A 329 LYS cc_start: 0.7521 (mttt) cc_final: 0.7131 (mtpm) REVERT: A 352 ASP cc_start: 0.7855 (m-30) cc_final: 0.7474 (m-30) REVERT: A 353 LYS cc_start: 0.6817 (ttpp) cc_final: 0.6399 (tptp) REVERT: A 357 LEU cc_start: 0.7306 (mt) cc_final: 0.6872 (mt) REVERT: A 367 LYS cc_start: 0.8337 (tttt) cc_final: 0.7983 (tttm) REVERT: A 380 TYR cc_start: 0.7482 (m-80) cc_final: 0.6993 (m-80) REVERT: A 409 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7160 (mtm) REVERT: A 412 LYS cc_start: 0.7688 (mtmt) cc_final: 0.7384 (mtpt) REVERT: A 416 ASP cc_start: 0.7680 (m-30) cc_final: 0.7275 (m-30) REVERT: A 435 LYS cc_start: 0.7424 (mttm) cc_final: 0.7094 (mttm) REVERT: B 31 ASP cc_start: 0.7428 (m-30) cc_final: 0.7036 (p0) REVERT: B 53 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7620 (mm-30) REVERT: B 57 LYS cc_start: 0.7653 (tttm) cc_final: 0.7189 (ttmt) REVERT: B 84 GLU cc_start: 0.7408 (tp30) cc_final: 0.7032 (mm-30) REVERT: B 90 TYR cc_start: 0.7591 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: B 107 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6373 (tp30) REVERT: B 220 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8668 (m-40) REVERT: B 240 ASP cc_start: 0.8045 (m-30) cc_final: 0.7661 (m-30) REVERT: B 293 HIS cc_start: 0.7432 (m-70) cc_final: 0.6280 (t-90) REVERT: B 313 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: B 325 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7544 (tp30) REVERT: B 329 LYS cc_start: 0.7521 (mttt) cc_final: 0.7129 (mtpm) REVERT: B 352 ASP cc_start: 0.7851 (m-30) cc_final: 0.7470 (m-30) REVERT: B 353 LYS cc_start: 0.6829 (ttpp) cc_final: 0.6414 (tptp) REVERT: B 357 LEU cc_start: 0.7321 (mt) cc_final: 0.6886 (mt) REVERT: B 367 LYS cc_start: 0.8337 (tttt) cc_final: 0.7984 (tttm) REVERT: B 380 TYR cc_start: 0.7473 (m-80) cc_final: 0.6974 (m-80) REVERT: B 409 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7127 (mtm) REVERT: B 416 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7167 (m-30) REVERT: B 435 LYS cc_start: 0.7430 (mttm) cc_final: 0.7106 (mttm) REVERT: C 31 ASP cc_start: 0.7422 (m-30) cc_final: 0.7024 (p0) REVERT: C 53 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7601 (mm-30) REVERT: C 57 LYS cc_start: 0.7660 (tttm) cc_final: 0.7195 (ttmt) REVERT: C 84 GLU cc_start: 0.7401 (tp30) cc_final: 0.7001 (mm-30) REVERT: C 90 TYR cc_start: 0.7613 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: C 107 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6332 (tp30) REVERT: C 220 ASN cc_start: 0.8907 (OUTLIER) cc_final: 0.8654 (m-40) REVERT: C 240 ASP cc_start: 0.8010 (m-30) cc_final: 0.7655 (m-30) REVERT: C 293 HIS cc_start: 0.7424 (m-70) cc_final: 0.6269 (t-90) REVERT: C 313 GLU cc_start: 0.7186 (pt0) cc_final: 0.6526 (pm20) REVERT: C 325 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7559 (tp30) REVERT: C 329 LYS cc_start: 0.7505 (mttt) cc_final: 0.7110 (mtpm) REVERT: C 352 ASP cc_start: 0.7837 (m-30) cc_final: 0.7458 (m-30) REVERT: C 353 LYS cc_start: 0.6833 (ttpp) cc_final: 0.6415 (tptp) REVERT: C 357 LEU cc_start: 0.7293 (mt) cc_final: 0.6860 (mt) REVERT: C 367 LYS cc_start: 0.8331 (tttt) cc_final: 0.7982 (tttm) REVERT: C 380 TYR cc_start: 0.7502 (m-80) cc_final: 0.7009 (m-80) REVERT: C 409 MET cc_start: 0.8219 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: C 416 ASP cc_start: 0.7647 (m-30) cc_final: 0.7195 (m-30) REVERT: C 435 LYS cc_start: 0.7448 (mttm) cc_final: 0.7100 (mttm) REVERT: D 31 ASP cc_start: 0.7408 (m-30) cc_final: 0.7022 (p0) REVERT: D 53 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7626 (mm-30) REVERT: D 57 LYS cc_start: 0.7647 (tttm) cc_final: 0.7192 (ttmt) REVERT: D 84 GLU cc_start: 0.7376 (tp30) cc_final: 0.7026 (mm-30) REVERT: D 90 TYR cc_start: 0.7601 (OUTLIER) cc_final: 0.6928 (m-80) REVERT: D 107 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6368 (tp30) REVERT: D 220 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8667 (m-40) REVERT: D 240 ASP cc_start: 0.8021 (m-30) cc_final: 0.7666 (m-30) REVERT: D 293 HIS cc_start: 0.7435 (m-70) cc_final: 0.6275 (t-90) REVERT: D 313 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6522 (pm20) REVERT: D 325 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7542 (tp30) REVERT: D 329 LYS cc_start: 0.7526 (mttt) cc_final: 0.7135 (mtpm) REVERT: D 352 ASP cc_start: 0.7844 (m-30) cc_final: 0.7463 (m-30) REVERT: D 353 LYS cc_start: 0.6822 (ttpp) cc_final: 0.6402 (tptp) REVERT: D 357 LEU cc_start: 0.7308 (mt) cc_final: 0.6872 (mt) REVERT: D 367 LYS cc_start: 0.8334 (tttt) cc_final: 0.7979 (tttm) REVERT: D 380 TYR cc_start: 0.7486 (m-80) cc_final: 0.7000 (m-80) REVERT: D 409 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7171 (mtm) REVERT: D 416 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: D 435 LYS cc_start: 0.7476 (mttm) cc_final: 0.7131 (mttm) outliers start: 51 outliers final: 13 residues processed: 310 average time/residue: 0.4987 time to fit residues: 171.4746 Evaluate side-chains 292 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 259 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 90 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 90 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 1 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 110 ASN A 117 ASN A 220 ASN B 19 GLN B 110 ASN B 117 ASN B 220 ASN C 19 GLN C 110 ASN C 117 ASN C 220 ASN D 19 GLN D 110 ASN D 117 ASN D 220 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.143066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.115015 restraints weight = 15424.373| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.36 r_work: 0.3113 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 15496 Z= 0.251 Angle : 0.607 7.563 20984 Z= 0.323 Chirality : 0.048 0.283 2324 Planarity : 0.005 0.031 2716 Dihedral : 4.992 21.627 2104 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.78 % Allowed : 19.42 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.19), residues: 1964 helix: 1.36 (0.18), residues: 804 sheet: 0.13 (0.26), residues: 408 loop : -0.08 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 326 TYR 0.025 0.003 TYR C 351 PHE 0.012 0.002 PHE D 483 TRP 0.009 0.002 TRP A 136 HIS 0.004 0.002 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00608 (15496) covalent geometry : angle 0.60718 (20984) hydrogen bonds : bond 0.04265 ( 720) hydrogen bonds : angle 5.26033 ( 2100) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 255 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7479 (m-30) cc_final: 0.7117 (p0) REVERT: A 53 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7657 (mm-30) REVERT: A 57 LYS cc_start: 0.7763 (tttm) cc_final: 0.7441 (tttp) REVERT: A 84 GLU cc_start: 0.7552 (tp30) cc_final: 0.7180 (mp0) REVERT: A 107 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.5731 (mm-30) REVERT: A 220 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8670 (m110) REVERT: A 240 ASP cc_start: 0.8012 (m-30) cc_final: 0.7658 (m-30) REVERT: A 293 HIS cc_start: 0.7517 (m-70) cc_final: 0.6368 (t-90) REVERT: A 325 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7550 (tp30) REVERT: A 329 LYS cc_start: 0.7543 (mttt) cc_final: 0.7060 (mtpm) REVERT: A 352 ASP cc_start: 0.7887 (m-30) cc_final: 0.7549 (m-30) REVERT: A 353 LYS cc_start: 0.6870 (ttpp) cc_final: 0.6452 (tptp) REVERT: A 357 LEU cc_start: 0.7327 (mt) cc_final: 0.6882 (mt) REVERT: A 367 LYS cc_start: 0.8387 (tttt) cc_final: 0.8024 (tttm) REVERT: A 380 TYR cc_start: 0.7557 (m-80) cc_final: 0.7048 (m-80) REVERT: A 409 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7256 (mtm) REVERT: A 412 LYS cc_start: 0.7701 (mtmt) cc_final: 0.7409 (mtpt) REVERT: A 416 ASP cc_start: 0.7701 (m-30) cc_final: 0.7307 (m-30) REVERT: A 435 LYS cc_start: 0.7594 (mttm) cc_final: 0.7323 (mttm) REVERT: B 31 ASP cc_start: 0.7459 (m-30) cc_final: 0.7110 (p0) REVERT: B 53 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7665 (mm-30) REVERT: B 57 LYS cc_start: 0.7745 (tttm) cc_final: 0.7417 (tttp) REVERT: B 84 GLU cc_start: 0.7514 (tp30) cc_final: 0.7168 (mp0) REVERT: B 107 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.5748 (mm-30) REVERT: B 220 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8678 (m110) REVERT: B 240 ASP cc_start: 0.8015 (m-30) cc_final: 0.7666 (m-30) REVERT: B 293 HIS cc_start: 0.7505 (m-70) cc_final: 0.6351 (t-90) REVERT: B 325 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7505 (tp30) REVERT: B 329 LYS cc_start: 0.7518 (mttt) cc_final: 0.7023 (mtpm) REVERT: B 352 ASP cc_start: 0.7904 (m-30) cc_final: 0.7567 (m-30) REVERT: B 353 LYS cc_start: 0.6900 (ttpp) cc_final: 0.6483 (tptp) REVERT: B 357 LEU cc_start: 0.7364 (mt) cc_final: 0.6918 (mt) REVERT: B 367 LYS cc_start: 0.8396 (tttt) cc_final: 0.8035 (tttm) REVERT: B 380 TYR cc_start: 0.7541 (m-80) cc_final: 0.7025 (m-80) REVERT: B 409 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7209 (mtm) REVERT: B 435 LYS cc_start: 0.7614 (mttm) cc_final: 0.7343 (mttm) REVERT: C 31 ASP cc_start: 0.7465 (m-30) cc_final: 0.7114 (p0) REVERT: C 53 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7664 (mm-30) REVERT: C 57 LYS cc_start: 0.7750 (tttm) cc_final: 0.7425 (tttp) REVERT: C 84 GLU cc_start: 0.7520 (tp30) cc_final: 0.7147 (mp0) REVERT: C 107 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.5740 (mm-30) REVERT: C 220 ASN cc_start: 0.8883 (OUTLIER) cc_final: 0.8677 (m110) REVERT: C 240 ASP cc_start: 0.7998 (m-30) cc_final: 0.7641 (m-30) REVERT: C 293 HIS cc_start: 0.7492 (m-70) cc_final: 0.6350 (t-90) REVERT: C 325 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7550 (tp30) REVERT: C 329 LYS cc_start: 0.7534 (mttt) cc_final: 0.7053 (mtpm) REVERT: C 352 ASP cc_start: 0.7886 (m-30) cc_final: 0.7547 (m-30) REVERT: C 353 LYS cc_start: 0.6891 (ttpp) cc_final: 0.6477 (tptp) REVERT: C 357 LEU cc_start: 0.7345 (mt) cc_final: 0.6903 (mt) REVERT: C 367 LYS cc_start: 0.8389 (tttt) cc_final: 0.8034 (tttm) REVERT: C 380 TYR cc_start: 0.7565 (m-80) cc_final: 0.7044 (m-80) REVERT: C 409 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7306 (mtt) REVERT: C 416 ASP cc_start: 0.7714 (m-30) cc_final: 0.7268 (m-30) REVERT: C 435 LYS cc_start: 0.7596 (mttm) cc_final: 0.7315 (mttm) REVERT: D 31 ASP cc_start: 0.7446 (m-30) cc_final: 0.7099 (p0) REVERT: D 53 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7658 (mm-30) REVERT: D 57 LYS cc_start: 0.7746 (tttm) cc_final: 0.7423 (tttp) REVERT: D 84 GLU cc_start: 0.7505 (tp30) cc_final: 0.7176 (mp0) REVERT: D 107 GLU cc_start: 0.6984 (OUTLIER) cc_final: 0.5739 (mm-30) REVERT: D 220 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8669 (m110) REVERT: D 240 ASP cc_start: 0.7978 (m-30) cc_final: 0.7624 (m-30) REVERT: D 293 HIS cc_start: 0.7515 (m-70) cc_final: 0.6355 (t-90) REVERT: D 325 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7535 (tp30) REVERT: D 329 LYS cc_start: 0.7476 (mttt) cc_final: 0.7073 (mtpm) REVERT: D 352 ASP cc_start: 0.7892 (m-30) cc_final: 0.7550 (m-30) REVERT: D 353 LYS cc_start: 0.6887 (ttpp) cc_final: 0.6466 (tptp) REVERT: D 357 LEU cc_start: 0.7360 (mt) cc_final: 0.6919 (mt) REVERT: D 367 LYS cc_start: 0.8402 (tttt) cc_final: 0.8043 (tttm) REVERT: D 380 TYR cc_start: 0.7567 (m-80) cc_final: 0.7049 (m-80) REVERT: D 409 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7293 (mtm) REVERT: D 416 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7215 (m-30) REVERT: D 435 LYS cc_start: 0.7643 (mttm) cc_final: 0.7363 (mttm) outliers start: 77 outliers final: 25 residues processed: 303 average time/residue: 0.5376 time to fit residues: 179.8014 Evaluate side-chains 289 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 251 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 138 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 121 optimal weight: 0.5980 chunk 137 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 117 ASN A 220 ASN B 19 GLN B 117 ASN B 220 ASN C 19 GLN C 117 ASN C 220 ASN D 19 GLN D 117 ASN D 220 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.144965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.118384 restraints weight = 15540.565| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.30 r_work: 0.3169 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15496 Z= 0.138 Angle : 0.528 7.238 20984 Z= 0.281 Chirality : 0.044 0.242 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.768 20.146 2104 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.98 % Allowed : 21.65 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.19), residues: 1964 helix: 1.55 (0.18), residues: 804 sheet: 0.20 (0.26), residues: 384 loop : -0.01 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 131 TYR 0.021 0.002 TYR B 351 PHE 0.008 0.001 PHE D 24 TRP 0.007 0.001 TRP C 178 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00328 (15496) covalent geometry : angle 0.52775 (20984) hydrogen bonds : bond 0.03575 ( 720) hydrogen bonds : angle 5.12088 ( 2100) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7455 (m-30) cc_final: 0.7003 (p0) REVERT: A 53 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7602 (mm-30) REVERT: A 57 LYS cc_start: 0.7674 (tttm) cc_final: 0.7358 (tttp) REVERT: A 84 GLU cc_start: 0.7427 (tp30) cc_final: 0.7022 (mm-30) REVERT: A 107 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6282 (tp30) REVERT: A 220 ASN cc_start: 0.8871 (OUTLIER) cc_final: 0.8607 (m110) REVERT: A 240 ASP cc_start: 0.7982 (m-30) cc_final: 0.7574 (m-30) REVERT: A 293 HIS cc_start: 0.7407 (m-70) cc_final: 0.6258 (t-90) REVERT: A 325 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7523 (tp30) REVERT: A 329 LYS cc_start: 0.7490 (mttt) cc_final: 0.7010 (mtpm) REVERT: A 352 ASP cc_start: 0.7843 (m-30) cc_final: 0.7497 (m-30) REVERT: A 353 LYS cc_start: 0.6798 (ttpp) cc_final: 0.6374 (tptt) REVERT: A 357 LEU cc_start: 0.7284 (mt) cc_final: 0.6790 (mt) REVERT: A 367 LYS cc_start: 0.8307 (tttt) cc_final: 0.7946 (tttm) REVERT: A 380 TYR cc_start: 0.7379 (m-80) cc_final: 0.6870 (m-80) REVERT: A 409 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7196 (mtm) REVERT: A 412 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7378 (mtpt) REVERT: A 416 ASP cc_start: 0.7632 (m-30) cc_final: 0.7213 (m-30) REVERT: A 435 LYS cc_start: 0.7483 (mttm) cc_final: 0.7207 (mttm) REVERT: A 481 TYR cc_start: 0.7030 (OUTLIER) cc_final: 0.6115 (m-80) REVERT: B 31 ASP cc_start: 0.7439 (m-30) cc_final: 0.6999 (p0) REVERT: B 53 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7621 (mm-30) REVERT: B 57 LYS cc_start: 0.7667 (tttm) cc_final: 0.7346 (tttp) REVERT: B 84 GLU cc_start: 0.7403 (tp30) cc_final: 0.7023 (mm-30) REVERT: B 107 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.6307 (tp30) REVERT: B 220 ASN cc_start: 0.8865 (OUTLIER) cc_final: 0.8605 (m110) REVERT: B 240 ASP cc_start: 0.7986 (m-30) cc_final: 0.7591 (m-30) REVERT: B 293 HIS cc_start: 0.7388 (m-70) cc_final: 0.6245 (t-90) REVERT: B 325 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7531 (tp30) REVERT: B 329 LYS cc_start: 0.7486 (mttt) cc_final: 0.6995 (mtpm) REVERT: B 352 ASP cc_start: 0.7846 (m-30) cc_final: 0.7497 (m-30) REVERT: B 353 LYS cc_start: 0.6808 (ttpp) cc_final: 0.6388 (tptt) REVERT: B 357 LEU cc_start: 0.7313 (mt) cc_final: 0.6820 (mt) REVERT: B 367 LYS cc_start: 0.8319 (tttt) cc_final: 0.7962 (tttm) REVERT: B 380 TYR cc_start: 0.7362 (m-80) cc_final: 0.6846 (m-80) REVERT: B 409 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7157 (mtm) REVERT: B 435 LYS cc_start: 0.7490 (mttm) cc_final: 0.7212 (mttm) REVERT: B 481 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: C 31 ASP cc_start: 0.7442 (m-30) cc_final: 0.6996 (p0) REVERT: C 53 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7608 (mm-30) REVERT: C 57 LYS cc_start: 0.7657 (tttm) cc_final: 0.7337 (tttp) REVERT: C 84 GLU cc_start: 0.7362 (tp30) cc_final: 0.6952 (mm-30) REVERT: C 107 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6297 (tp30) REVERT: C 220 ASN cc_start: 0.8861 (OUTLIER) cc_final: 0.8604 (m110) REVERT: C 240 ASP cc_start: 0.7976 (m-30) cc_final: 0.7599 (m-30) REVERT: C 293 HIS cc_start: 0.7390 (m-70) cc_final: 0.6258 (t-90) REVERT: C 325 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7499 (tp30) REVERT: C 329 LYS cc_start: 0.7474 (mttt) cc_final: 0.6991 (mtpm) REVERT: C 352 ASP cc_start: 0.7826 (m-30) cc_final: 0.7479 (m-30) REVERT: C 353 LYS cc_start: 0.6810 (ttpp) cc_final: 0.6394 (tptt) REVERT: C 357 LEU cc_start: 0.7301 (mt) cc_final: 0.6807 (mt) REVERT: C 367 LYS cc_start: 0.8308 (tttt) cc_final: 0.7954 (tttm) REVERT: C 380 TYR cc_start: 0.7387 (m-80) cc_final: 0.6870 (m-80) REVERT: C 409 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7193 (mtt) REVERT: C 416 ASP cc_start: 0.7646 (m-30) cc_final: 0.7167 (m-30) REVERT: C 435 LYS cc_start: 0.7471 (mttm) cc_final: 0.7199 (mttm) REVERT: C 481 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: D 31 ASP cc_start: 0.7426 (m-30) cc_final: 0.6990 (p0) REVERT: D 53 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7608 (mm-30) REVERT: D 57 LYS cc_start: 0.7656 (tttm) cc_final: 0.7337 (tttp) REVERT: D 84 GLU cc_start: 0.7402 (tp30) cc_final: 0.7034 (mm-30) REVERT: D 107 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.6285 (tp30) REVERT: D 220 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8603 (m110) REVERT: D 240 ASP cc_start: 0.7970 (m-30) cc_final: 0.7590 (m-30) REVERT: D 293 HIS cc_start: 0.7402 (m-70) cc_final: 0.6253 (t-90) REVERT: D 325 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7498 (tp30) REVERT: D 329 LYS cc_start: 0.7493 (mttt) cc_final: 0.7019 (mtpm) REVERT: D 352 ASP cc_start: 0.7850 (m-30) cc_final: 0.7503 (m-30) REVERT: D 353 LYS cc_start: 0.6791 (ttpp) cc_final: 0.6374 (tptt) REVERT: D 357 LEU cc_start: 0.7313 (mt) cc_final: 0.6820 (mt) REVERT: D 367 LYS cc_start: 0.8329 (tttt) cc_final: 0.7972 (tttm) REVERT: D 380 TYR cc_start: 0.7377 (m-80) cc_final: 0.6861 (m-80) REVERT: D 409 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7193 (mtm) REVERT: D 435 LYS cc_start: 0.7499 (mttm) cc_final: 0.7227 (mttm) REVERT: D 481 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6109 (m-80) outliers start: 48 outliers final: 23 residues processed: 288 average time/residue: 0.5141 time to fit residues: 163.8163 Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 181 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 220 ASN B 19 GLN B 220 ASN C 19 GLN C 220 ASN D 19 GLN D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.145474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118849 restraints weight = 15462.117| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.36 r_work: 0.3164 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15496 Z= 0.153 Angle : 0.534 8.300 20984 Z= 0.285 Chirality : 0.044 0.229 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.707 19.670 2104 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 21.90 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.19), residues: 1964 helix: 1.55 (0.18), residues: 804 sheet: 0.18 (0.27), residues: 384 loop : 0.03 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 131 TYR 0.021 0.002 TYR C 351 PHE 0.009 0.001 PHE A 24 TRP 0.007 0.001 TRP C 178 HIS 0.003 0.001 HIS A 30 Details of bonding type rmsd covalent geometry : bond 0.00371 (15496) covalent geometry : angle 0.53409 (20984) hydrogen bonds : bond 0.03601 ( 720) hydrogen bonds : angle 5.06113 ( 2100) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 248 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7444 (m-30) cc_final: 0.6995 (p0) REVERT: A 53 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7568 (mm-30) REVERT: A 57 LYS cc_start: 0.7674 (tttm) cc_final: 0.7304 (tttt) REVERT: A 84 GLU cc_start: 0.7381 (tp30) cc_final: 0.6975 (mm-30) REVERT: A 107 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6294 (tp30) REVERT: A 220 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8664 (m110) REVERT: A 240 ASP cc_start: 0.7980 (m-30) cc_final: 0.7577 (m-30) REVERT: A 293 HIS cc_start: 0.7405 (m-70) cc_final: 0.6252 (t-90) REVERT: A 325 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7553 (tp30) REVERT: A 329 LYS cc_start: 0.7496 (mttt) cc_final: 0.7080 (mtpm) REVERT: A 352 ASP cc_start: 0.7861 (m-30) cc_final: 0.7517 (m-30) REVERT: A 353 LYS cc_start: 0.6805 (ttpp) cc_final: 0.6387 (tptt) REVERT: A 357 LEU cc_start: 0.7302 (mt) cc_final: 0.6833 (mt) REVERT: A 367 LYS cc_start: 0.8316 (tttt) cc_final: 0.7959 (tttm) REVERT: A 380 TYR cc_start: 0.7389 (m-80) cc_final: 0.6923 (m-80) REVERT: A 409 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7195 (mtm) REVERT: A 412 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7363 (mtpt) REVERT: A 416 ASP cc_start: 0.7634 (m-30) cc_final: 0.7193 (m-30) REVERT: A 435 LYS cc_start: 0.7476 (mttm) cc_final: 0.7254 (mttm) REVERT: A 481 TYR cc_start: 0.7032 (OUTLIER) cc_final: 0.6126 (m-80) REVERT: B 31 ASP cc_start: 0.7433 (m-30) cc_final: 0.6997 (p0) REVERT: B 53 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7590 (mm-30) REVERT: B 57 LYS cc_start: 0.7670 (tttm) cc_final: 0.7297 (tttt) REVERT: B 84 GLU cc_start: 0.7418 (tp30) cc_final: 0.7033 (mm-30) REVERT: B 107 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6331 (tp30) REVERT: B 220 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8658 (m110) REVERT: B 240 ASP cc_start: 0.8005 (m-30) cc_final: 0.7613 (m-30) REVERT: B 293 HIS cc_start: 0.7386 (m-70) cc_final: 0.6236 (t-90) REVERT: B 325 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7523 (tp30) REVERT: B 329 LYS cc_start: 0.7505 (mttt) cc_final: 0.7089 (mtpm) REVERT: B 352 ASP cc_start: 0.7866 (m-30) cc_final: 0.7521 (m-30) REVERT: B 353 LYS cc_start: 0.6825 (ttpp) cc_final: 0.6410 (tptt) REVERT: B 357 LEU cc_start: 0.7337 (mt) cc_final: 0.6867 (mt) REVERT: B 367 LYS cc_start: 0.8320 (tttt) cc_final: 0.7962 (tttm) REVERT: B 380 TYR cc_start: 0.7372 (m-80) cc_final: 0.6908 (m-80) REVERT: B 409 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7151 (mtm) REVERT: B 435 LYS cc_start: 0.7473 (mttm) cc_final: 0.7247 (mttm) REVERT: B 481 TYR cc_start: 0.7046 (OUTLIER) cc_final: 0.6134 (m-80) REVERT: C 31 ASP cc_start: 0.7429 (m-30) cc_final: 0.6989 (p0) REVERT: C 53 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7575 (mm-30) REVERT: C 57 LYS cc_start: 0.7672 (tttm) cc_final: 0.7299 (tttt) REVERT: C 84 GLU cc_start: 0.7377 (tp30) cc_final: 0.6960 (mm-30) REVERT: C 107 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6321 (tp30) REVERT: C 220 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8667 (m110) REVERT: C 240 ASP cc_start: 0.7978 (m-30) cc_final: 0.7584 (m-30) REVERT: C 293 HIS cc_start: 0.7374 (m-70) cc_final: 0.6236 (t-90) REVERT: C 325 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7539 (tp30) REVERT: C 329 LYS cc_start: 0.7497 (mttt) cc_final: 0.7083 (mtpm) REVERT: C 352 ASP cc_start: 0.7836 (m-30) cc_final: 0.7493 (m-30) REVERT: C 353 LYS cc_start: 0.6824 (ttpp) cc_final: 0.6408 (tptt) REVERT: C 357 LEU cc_start: 0.7329 (mt) cc_final: 0.6862 (mt) REVERT: C 367 LYS cc_start: 0.8316 (tttt) cc_final: 0.7965 (tttm) REVERT: C 380 TYR cc_start: 0.7375 (m-80) cc_final: 0.6901 (m-80) REVERT: C 409 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7226 (mtt) REVERT: C 416 ASP cc_start: 0.7669 (m-30) cc_final: 0.7179 (m-30) REVERT: C 435 LYS cc_start: 0.7466 (mttm) cc_final: 0.7234 (mttm) REVERT: C 481 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.6158 (m-80) REVERT: D 31 ASP cc_start: 0.7416 (m-30) cc_final: 0.6987 (p0) REVERT: D 53 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 57 LYS cc_start: 0.7658 (tttm) cc_final: 0.7289 (tttt) REVERT: D 84 GLU cc_start: 0.7412 (tp30) cc_final: 0.7036 (mm-30) REVERT: D 107 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6313 (tp30) REVERT: D 220 ASN cc_start: 0.8949 (OUTLIER) cc_final: 0.8658 (m110) REVERT: D 240 ASP cc_start: 0.7979 (m-30) cc_final: 0.7583 (m-30) REVERT: D 293 HIS cc_start: 0.7385 (m-70) cc_final: 0.6227 (t-90) REVERT: D 325 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7541 (tp30) REVERT: D 329 LYS cc_start: 0.7502 (mttt) cc_final: 0.7100 (mtpm) REVERT: D 352 ASP cc_start: 0.7871 (m-30) cc_final: 0.7528 (m-30) REVERT: D 353 LYS cc_start: 0.6808 (ttpp) cc_final: 0.6397 (tptt) REVERT: D 357 LEU cc_start: 0.7343 (mt) cc_final: 0.6874 (mt) REVERT: D 367 LYS cc_start: 0.8329 (tttt) cc_final: 0.7975 (tttm) REVERT: D 380 TYR cc_start: 0.7366 (m-80) cc_final: 0.6890 (m-80) REVERT: D 409 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7190 (mtm) REVERT: D 435 LYS cc_start: 0.7478 (mttm) cc_final: 0.7247 (mttm) REVERT: D 481 TYR cc_start: 0.7037 (OUTLIER) cc_final: 0.6136 (m-80) outliers start: 44 outliers final: 22 residues processed: 278 average time/residue: 0.5240 time to fit residues: 160.8139 Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 107 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 220 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 19 GLN C 220 ASN D 19 GLN D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.145716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117597 restraints weight = 15608.603| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.38 r_work: 0.3165 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15496 Z= 0.142 Angle : 0.527 7.346 20984 Z= 0.280 Chirality : 0.044 0.223 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.648 19.391 2104 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.54 % Allowed : 22.64 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 1964 helix: 1.61 (0.19), residues: 804 sheet: 0.15 (0.27), residues: 384 loop : 0.06 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 131 TYR 0.020 0.002 TYR D 351 PHE 0.009 0.001 PHE B 24 TRP 0.007 0.001 TRP C 178 HIS 0.002 0.001 HIS C 30 Details of bonding type rmsd covalent geometry : bond 0.00343 (15496) covalent geometry : angle 0.52694 (20984) hydrogen bonds : bond 0.03508 ( 720) hydrogen bonds : angle 5.01553 ( 2100) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7456 (m-30) cc_final: 0.7009 (p0) REVERT: A 53 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7596 (mm-30) REVERT: A 57 LYS cc_start: 0.7691 (tttm) cc_final: 0.7314 (tttt) REVERT: A 84 GLU cc_start: 0.7409 (tp30) cc_final: 0.6998 (mm-30) REVERT: A 90 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.6929 (m-80) REVERT: A 107 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6346 (tp30) REVERT: A 220 ASN cc_start: 0.8958 (OUTLIER) cc_final: 0.8673 (m110) REVERT: A 240 ASP cc_start: 0.8003 (m-30) cc_final: 0.7609 (m-30) REVERT: A 293 HIS cc_start: 0.7411 (m-70) cc_final: 0.6250 (t-90) REVERT: A 325 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7602 (tp30) REVERT: A 329 LYS cc_start: 0.7475 (mttt) cc_final: 0.7084 (mtpm) REVERT: A 352 ASP cc_start: 0.7877 (m-30) cc_final: 0.7538 (m-30) REVERT: A 353 LYS cc_start: 0.6822 (ttpp) cc_final: 0.6400 (tptt) REVERT: A 357 LEU cc_start: 0.7311 (mt) cc_final: 0.6845 (mt) REVERT: A 367 LYS cc_start: 0.8319 (tttt) cc_final: 0.7968 (tttm) REVERT: A 380 TYR cc_start: 0.7356 (m-80) cc_final: 0.6868 (m-80) REVERT: A 409 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7229 (mtm) REVERT: A 412 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7367 (mtpt) REVERT: A 416 ASP cc_start: 0.7657 (m-30) cc_final: 0.7211 (m-30) REVERT: A 435 LYS cc_start: 0.7445 (mttm) cc_final: 0.7240 (mttm) REVERT: A 481 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6131 (m-80) REVERT: B 31 ASP cc_start: 0.7442 (m-30) cc_final: 0.7007 (p0) REVERT: B 53 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7618 (mm-30) REVERT: B 57 LYS cc_start: 0.7679 (tttm) cc_final: 0.7300 (tttt) REVERT: B 84 GLU cc_start: 0.7401 (tp30) cc_final: 0.7013 (mm-30) REVERT: B 107 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6379 (tp30) REVERT: B 220 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8664 (m110) REVERT: B 240 ASP cc_start: 0.8025 (m-30) cc_final: 0.7641 (m-30) REVERT: B 293 HIS cc_start: 0.7391 (m-70) cc_final: 0.6231 (t-90) REVERT: B 325 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7567 (tp30) REVERT: B 329 LYS cc_start: 0.7479 (mttt) cc_final: 0.7079 (mtpm) REVERT: B 352 ASP cc_start: 0.7882 (m-30) cc_final: 0.7540 (m-30) REVERT: B 353 LYS cc_start: 0.6830 (ttpp) cc_final: 0.6417 (tptt) REVERT: B 357 LEU cc_start: 0.7341 (mt) cc_final: 0.6874 (mt) REVERT: B 367 LYS cc_start: 0.8332 (tttt) cc_final: 0.7990 (tttm) REVERT: B 380 TYR cc_start: 0.7349 (m-80) cc_final: 0.6858 (m-80) REVERT: B 409 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7158 (mtm) REVERT: B 435 LYS cc_start: 0.7446 (mttm) cc_final: 0.7231 (mttm) REVERT: B 481 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.6127 (m-80) REVERT: C 31 ASP cc_start: 0.7435 (m-30) cc_final: 0.6999 (p0) REVERT: C 53 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7605 (mm-30) REVERT: C 57 LYS cc_start: 0.7688 (tttm) cc_final: 0.7307 (tttt) REVERT: C 84 GLU cc_start: 0.7419 (tp30) cc_final: 0.6990 (mm-30) REVERT: C 90 TYR cc_start: 0.7550 (OUTLIER) cc_final: 0.6920 (m-80) REVERT: C 107 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6374 (tp30) REVERT: C 220 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8675 (m110) REVERT: C 240 ASP cc_start: 0.8016 (m-30) cc_final: 0.7644 (m-30) REVERT: C 293 HIS cc_start: 0.7378 (m-70) cc_final: 0.6238 (t-90) REVERT: C 325 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7583 (tp30) REVERT: C 329 LYS cc_start: 0.7476 (mttt) cc_final: 0.7080 (mtpm) REVERT: C 352 ASP cc_start: 0.7843 (m-30) cc_final: 0.7504 (m-30) REVERT: C 353 LYS cc_start: 0.6831 (ttpp) cc_final: 0.6417 (tptt) REVERT: C 357 LEU cc_start: 0.7332 (mt) cc_final: 0.6868 (mt) REVERT: C 367 LYS cc_start: 0.8318 (tttt) cc_final: 0.7979 (tttm) REVERT: C 380 TYR cc_start: 0.7367 (m-80) cc_final: 0.6874 (m-80) REVERT: C 409 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7229 (mtt) REVERT: C 416 ASP cc_start: 0.7691 (m-30) cc_final: 0.7203 (m-30) REVERT: C 435 LYS cc_start: 0.7448 (mttm) cc_final: 0.7232 (mttm) REVERT: C 481 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: D 31 ASP cc_start: 0.7435 (m-30) cc_final: 0.7000 (p0) REVERT: D 53 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 57 LYS cc_start: 0.7683 (tttm) cc_final: 0.7307 (tttt) REVERT: D 84 GLU cc_start: 0.7411 (tp30) cc_final: 0.7021 (mm-30) REVERT: D 107 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6346 (tp30) REVERT: D 220 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8671 (m110) REVERT: D 240 ASP cc_start: 0.8000 (m-30) cc_final: 0.7612 (m-30) REVERT: D 293 HIS cc_start: 0.7402 (m-70) cc_final: 0.6241 (t-90) REVERT: D 325 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7562 (tp30) REVERT: D 329 LYS cc_start: 0.7480 (mttt) cc_final: 0.7099 (mtpm) REVERT: D 352 ASP cc_start: 0.7893 (m-30) cc_final: 0.7554 (m-30) REVERT: D 353 LYS cc_start: 0.6816 (ttpp) cc_final: 0.6403 (tptt) REVERT: D 357 LEU cc_start: 0.7335 (mt) cc_final: 0.6868 (mt) REVERT: D 367 LYS cc_start: 0.8332 (tttt) cc_final: 0.7985 (tttm) REVERT: D 380 TYR cc_start: 0.7342 (m-80) cc_final: 0.6846 (m-80) REVERT: D 409 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7204 (mtm) REVERT: D 435 LYS cc_start: 0.7467 (mttm) cc_final: 0.7248 (mttm) REVERT: D 481 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6121 (m-80) outliers start: 41 outliers final: 22 residues processed: 276 average time/residue: 0.5363 time to fit residues: 163.1454 Evaluate side-chains 282 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 242 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 266 VAL Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 266 VAL Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 CYS Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 147 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 266 VAL Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 481 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 113 optimal weight: 0.0370 chunk 85 optimal weight: 0.9980 chunk 184 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 185 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.146747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.118824 restraints weight = 15456.774| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.37 r_work: 0.3176 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15496 Z= 0.118 Angle : 0.504 6.591 20984 Z= 0.269 Chirality : 0.043 0.219 2324 Planarity : 0.004 0.031 2716 Dihedral : 4.528 18.882 2104 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.73 % Allowed : 22.64 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.19), residues: 1964 helix: 1.70 (0.19), residues: 804 sheet: 0.10 (0.27), residues: 396 loop : 0.05 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 131 TYR 0.017 0.002 TYR C 351 PHE 0.007 0.001 PHE A 24 TRP 0.007 0.001 TRP C 453 HIS 0.002 0.001 HIS B 30 Details of bonding type rmsd covalent geometry : bond 0.00280 (15496) covalent geometry : angle 0.50449 (20984) hydrogen bonds : bond 0.03336 ( 720) hydrogen bonds : angle 4.93870 ( 2100) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5039.72 seconds wall clock time: 86 minutes 43.32 seconds (5203.32 seconds total)