Starting phenix.real_space_refine on Sat May 17 04:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvh_17966/05_2025/8pvh_17966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvh_17966/05_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_17966/05_2025/8pvh_17966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvh_17966/05_2025/8pvh_17966.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvh_17966/05_2025/8pvh_17966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvh_17966/05_2025/8pvh_17966.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 1, 'ASP: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: C, B, D Time building chain proxies: 8.12, per 1000 atoms: 0.54 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: 3.57 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.11 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: 5.21 Time building geometry restraints manager: 4.20 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.800 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (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 TRP 0.040 0.008 TRP A 178 HIS 0.012 0.004 HIS B 204 PHE 0.038 0.008 PHE A 151 TYR 0.037 0.008 TYR B 481 ARG 0.045 0.007 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.19383 ( 720) hydrogen bonds : angle 7.19745 ( 2100) covalent geometry : bond 0.00963 (15496) covalent geometry : angle 1.69471 (20984) *********************** 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 : 1.542 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: 1.4649 time to fit residues: 777.6318 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 : 1.562 ------------------------------------------------------------------------------- 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 165 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.149290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120504 restraints weight = 14818.374| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.30 r_work: 0.3200 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 15496 Z= 0.137 Angle : 0.570 6.462 20984 Z= 0.313 Chirality : 0.046 0.235 2324 Planarity : 0.004 0.035 2716 Dihedral : 5.292 18.732 2120 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.92 % Allowed : 14.08 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.18), residues: 1964 helix: 0.96 (0.17), residues: 816 sheet: 0.44 (0.25), residues: 412 loop : 0.05 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 178 HIS 0.002 0.001 HIS A 236 PHE 0.008 0.002 PHE C 38 TYR 0.016 0.002 TYR C 20 ARG 0.004 0.001 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 720) hydrogen bonds : angle 5.39700 ( 2100) covalent geometry : bond 0.00301 (15496) covalent geometry : angle 0.56987 (20984) *********************** 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 371 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 324 time to evaluate : 1.540 Fit side-chains REVERT: A 31 ASP cc_start: 0.7382 (m-30) cc_final: 0.7052 (p0) REVERT: A 53 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 57 LYS cc_start: 0.7790 (tttm) cc_final: 0.7406 (tttp) REVERT: A 84 GLU cc_start: 0.7568 (tp30) cc_final: 0.7032 (mm-30) REVERT: A 98 ARG cc_start: 0.7930 (ttp-170) cc_final: 0.7617 (ttp-170) REVERT: A 107 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5715 (mm-30) REVERT: A 117 ASN cc_start: 0.7909 (m-40) cc_final: 0.7505 (m-40) REVERT: A 119 TYR cc_start: 0.8292 (t80) cc_final: 0.7852 (t80) REVERT: A 158 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7257 (tt0) REVERT: A 193 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8128 (tmmt) REVERT: A 240 ASP cc_start: 0.7959 (m-30) cc_final: 0.7635 (m-30) REVERT: A 253 LEU cc_start: 0.8144 (mt) cc_final: 0.7855 (mm) REVERT: A 293 HIS cc_start: 0.7428 (m-70) cc_final: 0.6304 (t-90) REVERT: A 295 VAL cc_start: 0.8220 (p) cc_final: 0.7744 (t) REVERT: A 325 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7601 (tp30) REVERT: A 329 LYS cc_start: 0.7750 (mttt) cc_final: 0.7302 (mtpm) REVERT: A 357 LEU cc_start: 0.7299 (mt) cc_final: 0.6695 (mt) REVERT: A 367 LYS cc_start: 0.8284 (tttt) cc_final: 0.7868 (tttm) REVERT: A 380 TYR cc_start: 0.7503 (m-80) cc_final: 0.6874 (m-80) REVERT: A 416 ASP cc_start: 0.6652 (t70) cc_final: 0.6344 (t0) REVERT: A 442 THR cc_start: 0.8432 (m) cc_final: 0.8137 (m) REVERT: B 31 ASP cc_start: 0.7373 (m-30) cc_final: 0.7040 (p0) REVERT: B 53 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7821 (mm-30) REVERT: B 57 LYS cc_start: 0.7799 (tttm) cc_final: 0.7418 (tttp) REVERT: B 84 GLU cc_start: 0.7546 (tp30) cc_final: 0.7018 (mm-30) REVERT: B 98 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7609 (ttp-170) REVERT: B 107 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5731 (mm-30) REVERT: B 117 ASN cc_start: 0.7894 (m-40) cc_final: 0.7501 (m-40) REVERT: B 119 TYR cc_start: 0.8286 (t80) cc_final: 0.7847 (t80) REVERT: B 158 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7262 (tt0) REVERT: B 193 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8131 (tmmt) REVERT: B 240 ASP cc_start: 0.7962 (m-30) cc_final: 0.7640 (m-30) REVERT: B 253 LEU cc_start: 0.8158 (mt) cc_final: 0.7869 (mm) REVERT: B 293 HIS cc_start: 0.7428 (m-70) cc_final: 0.6305 (t-90) REVERT: B 295 VAL cc_start: 0.8218 (p) cc_final: 0.7744 (t) REVERT: B 325 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7577 (tp30) REVERT: B 329 LYS cc_start: 0.7753 (mttt) cc_final: 0.7303 (mtpm) REVERT: B 352 ASP cc_start: 0.7593 (m-30) cc_final: 0.7231 (m-30) REVERT: B 357 LEU cc_start: 0.7281 (mt) cc_final: 0.6672 (mt) REVERT: B 367 LYS cc_start: 0.8272 (tttt) cc_final: 0.7850 (tttm) REVERT: B 380 TYR cc_start: 0.7509 (m-80) cc_final: 0.6887 (m-80) REVERT: B 416 ASP cc_start: 0.6651 (t70) cc_final: 0.6341 (t0) REVERT: B 442 THR cc_start: 0.8440 (m) cc_final: 0.8142 (m) REVERT: C 31 ASP cc_start: 0.7385 (m-30) cc_final: 0.7056 (p0) REVERT: C 53 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 57 LYS cc_start: 0.7781 (tttm) cc_final: 0.7421 (tttp) REVERT: C 84 GLU cc_start: 0.7580 (tp30) cc_final: 0.7028 (mm-30) REVERT: C 98 ARG cc_start: 0.7932 (ttp-170) cc_final: 0.7616 (ttp-170) REVERT: C 107 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5726 (mm-30) REVERT: C 117 ASN cc_start: 0.7907 (m-40) cc_final: 0.7501 (m-40) REVERT: C 119 TYR cc_start: 0.8284 (t80) cc_final: 0.7844 (t80) REVERT: C 158 GLU cc_start: 0.7621 (mt-10) cc_final: 0.7261 (tt0) REVERT: C 240 ASP cc_start: 0.7950 (m-30) cc_final: 0.7625 (m-30) REVERT: C 253 LEU cc_start: 0.8146 (mt) cc_final: 0.7858 (mm) REVERT: C 285 ASP cc_start: 0.7262 (t0) cc_final: 0.7061 (p0) REVERT: C 293 HIS cc_start: 0.7430 (m-70) cc_final: 0.6303 (t-90) REVERT: C 295 VAL cc_start: 0.8219 (p) cc_final: 0.7742 (t) REVERT: C 325 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7587 (tp30) REVERT: C 329 LYS cc_start: 0.7752 (mttt) cc_final: 0.7305 (mtpm) REVERT: C 357 LEU cc_start: 0.7279 (mt) cc_final: 0.6679 (mt) REVERT: C 367 LYS cc_start: 0.8272 (tttt) cc_final: 0.7848 (tttm) REVERT: C 380 TYR cc_start: 0.7500 (m-80) cc_final: 0.6868 (m-80) REVERT: C 416 ASP cc_start: 0.6675 (t70) cc_final: 0.6359 (t0) REVERT: C 436 ASP cc_start: 0.7423 (t70) cc_final: 0.7213 (t0) REVERT: C 442 THR cc_start: 0.8434 (m) cc_final: 0.8136 (m) REVERT: D 31 ASP cc_start: 0.7403 (m-30) cc_final: 0.7060 (p0) REVERT: D 53 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7832 (mm-30) REVERT: D 57 LYS cc_start: 0.7795 (tttm) cc_final: 0.7431 (tttp) REVERT: D 84 GLU cc_start: 0.7543 (tp30) cc_final: 0.7002 (mm-30) REVERT: D 98 ARG cc_start: 0.7921 (ttp-170) cc_final: 0.7610 (ttp-170) REVERT: D 107 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5733 (mm-30) REVERT: D 117 ASN cc_start: 0.7900 (m-40) cc_final: 0.7501 (m-40) REVERT: D 119 TYR cc_start: 0.8285 (t80) cc_final: 0.7847 (t80) REVERT: D 158 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7257 (tt0) REVERT: D 193 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8131 (tmmt) REVERT: D 240 ASP cc_start: 0.7948 (m-30) cc_final: 0.7627 (m-30) REVERT: D 253 LEU cc_start: 0.8162 (mt) cc_final: 0.7878 (mm) REVERT: D 293 HIS cc_start: 0.7424 (m-70) cc_final: 0.6293 (t-90) REVERT: D 295 VAL cc_start: 0.8218 (p) cc_final: 0.7744 (t) REVERT: D 325 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7585 (tp30) REVERT: D 329 LYS cc_start: 0.7748 (mttt) cc_final: 0.7296 (mtpm) REVERT: D 352 ASP cc_start: 0.7596 (m-30) cc_final: 0.7236 (m-30) REVERT: D 357 LEU cc_start: 0.7287 (mt) cc_final: 0.6690 (mt) REVERT: D 367 LYS cc_start: 0.8294 (tttt) cc_final: 0.7880 (tttm) REVERT: D 380 TYR cc_start: 0.7484 (m-80) cc_final: 0.6856 (m-80) REVERT: D 416 ASP cc_start: 0.6680 (t70) cc_final: 0.6365 (t0) REVERT: D 436 ASP cc_start: 0.7425 (t70) cc_final: 0.7216 (t0) REVERT: D 442 THR cc_start: 0.8448 (m) cc_final: 0.8149 (m) outliers start: 47 outliers final: 4 residues processed: 359 average time/residue: 1.1938 time to fit residues: 473.0570 Evaluate side-chains 264 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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 193 LYS 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 C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU 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 125 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.147725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.118744 restraints weight = 15007.343| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.32 r_work: 0.3163 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 15496 Z= 0.160 Angle : 0.556 6.909 20984 Z= 0.297 Chirality : 0.046 0.164 2324 Planarity : 0.004 0.034 2716 Dihedral : 4.923 21.317 2104 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.85 % Allowed : 16.69 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 1964 helix: 1.32 (0.18), residues: 824 sheet: 0.26 (0.25), residues: 420 loop : 0.26 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 178 HIS 0.005 0.001 HIS C 236 PHE 0.011 0.002 PHE B 483 TYR 0.014 0.002 TYR C 20 ARG 0.006 0.001 ARG B 321 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 720) hydrogen bonds : angle 5.19125 ( 2100) covalent geometry : bond 0.00376 (15496) covalent geometry : angle 0.55556 (20984) *********************** 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 343 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 297 time to evaluate : 1.585 Fit side-chains REVERT: A 31 ASP cc_start: 0.7390 (m-30) cc_final: 0.7049 (p0) REVERT: A 53 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7774 (mm-30) REVERT: A 57 LYS cc_start: 0.7787 (tttm) cc_final: 0.7227 (ttmt) REVERT: A 69 GLN cc_start: 0.8104 (tp-100) cc_final: 0.7844 (tm-30) REVERT: A 84 GLU cc_start: 0.7404 (tp30) cc_final: 0.6905 (mm-30) REVERT: A 98 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7654 (ttp-170) REVERT: A 107 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6322 (tp30) REVERT: A 117 ASN cc_start: 0.8045 (m-40) cc_final: 0.7675 (m-40) REVERT: A 240 ASP cc_start: 0.7862 (m-30) cc_final: 0.7570 (m-30) REVERT: A 269 GLU cc_start: 0.7129 (tp30) cc_final: 0.6675 (tt0) REVERT: A 293 HIS cc_start: 0.7441 (m-70) cc_final: 0.6303 (t-90) REVERT: A 325 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7475 (tp30) REVERT: A 329 LYS cc_start: 0.7770 (mttt) cc_final: 0.7301 (mtpm) REVERT: A 352 ASP cc_start: 0.7879 (m-30) cc_final: 0.7492 (m-30) REVERT: A 353 LYS cc_start: 0.6730 (ttpp) cc_final: 0.6498 (tptp) REVERT: A 367 LYS cc_start: 0.8314 (tttt) cc_final: 0.7904 (tttm) REVERT: A 380 TYR cc_start: 0.7556 (m-80) cc_final: 0.7039 (m-80) REVERT: A 409 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7408 (mtt) REVERT: A 412 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7217 (mtpt) REVERT: A 477 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 31 ASP cc_start: 0.7381 (m-30) cc_final: 0.7042 (p0) REVERT: B 53 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 57 LYS cc_start: 0.7790 (tttm) cc_final: 0.7232 (ttmt) REVERT: B 69 GLN cc_start: 0.8105 (tp-100) cc_final: 0.7842 (tm-30) REVERT: B 84 GLU cc_start: 0.7384 (tp30) cc_final: 0.6876 (mm-30) REVERT: B 98 ARG cc_start: 0.7986 (ttp-170) cc_final: 0.7659 (ttp-170) REVERT: B 107 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: B 117 ASN cc_start: 0.8066 (m-40) cc_final: 0.7690 (m-40) REVERT: B 240 ASP cc_start: 0.7863 (m-30) cc_final: 0.7571 (m-30) REVERT: B 269 GLU cc_start: 0.7126 (tp30) cc_final: 0.6681 (tt0) REVERT: B 293 HIS cc_start: 0.7449 (m-70) cc_final: 0.6317 (t-90) REVERT: B 325 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7477 (tp30) REVERT: B 329 LYS cc_start: 0.7761 (mttt) cc_final: 0.7291 (mtpm) REVERT: B 352 ASP cc_start: 0.7872 (m-30) cc_final: 0.7483 (m-30) REVERT: B 353 LYS cc_start: 0.6730 (ttpp) cc_final: 0.6496 (tptp) REVERT: B 367 LYS cc_start: 0.8304 (tttt) cc_final: 0.7891 (tttm) REVERT: B 380 TYR cc_start: 0.7556 (m-80) cc_final: 0.7034 (m-80) REVERT: B 409 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7423 (mtt) REVERT: B 412 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7223 (mtpt) REVERT: B 477 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8002 (mt-10) REVERT: C 31 ASP cc_start: 0.7399 (m-30) cc_final: 0.7052 (p0) REVERT: C 53 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7790 (mm-30) REVERT: C 57 LYS cc_start: 0.7783 (tttm) cc_final: 0.7203 (ttmt) REVERT: C 69 GLN cc_start: 0.8102 (tp-100) cc_final: 0.7841 (tm-30) REVERT: C 84 GLU cc_start: 0.7412 (tp30) cc_final: 0.6910 (mm-30) REVERT: C 98 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7635 (ttp-170) REVERT: C 107 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6299 (tp30) REVERT: C 117 ASN cc_start: 0.8049 (m-40) cc_final: 0.7680 (m-40) REVERT: C 240 ASP cc_start: 0.7854 (m-30) cc_final: 0.7562 (m-30) REVERT: C 269 GLU cc_start: 0.7152 (tp30) cc_final: 0.6695 (tt0) REVERT: C 293 HIS cc_start: 0.7460 (m-70) cc_final: 0.6309 (t-90) REVERT: C 325 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7493 (tp30) REVERT: C 329 LYS cc_start: 0.7781 (mttt) cc_final: 0.7300 (mtpm) REVERT: C 352 ASP cc_start: 0.7863 (m-30) cc_final: 0.7474 (m-30) REVERT: C 353 LYS cc_start: 0.6723 (ttpp) cc_final: 0.6496 (tptp) REVERT: C 367 LYS cc_start: 0.8324 (tttt) cc_final: 0.7915 (tttm) REVERT: C 380 TYR cc_start: 0.7585 (m-80) cc_final: 0.7043 (m-80) REVERT: C 409 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7397 (mtt) REVERT: C 435 LYS cc_start: 0.7529 (mttm) cc_final: 0.7320 (mttm) REVERT: C 477 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8002 (mt-10) REVERT: D 31 ASP cc_start: 0.7382 (m-30) cc_final: 0.7031 (p0) REVERT: D 53 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7775 (mm-30) REVERT: D 57 LYS cc_start: 0.7790 (tttm) cc_final: 0.7211 (ttmt) REVERT: D 69 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7847 (tm-30) REVERT: D 84 GLU cc_start: 0.7368 (tp30) cc_final: 0.6880 (mm-30) REVERT: D 98 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7652 (ttp-170) REVERT: D 107 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6322 (tp30) REVERT: D 117 ASN cc_start: 0.8053 (m-40) cc_final: 0.7681 (m-40) REVERT: D 240 ASP cc_start: 0.7872 (m-30) cc_final: 0.7580 (m-30) REVERT: D 269 GLU cc_start: 0.7165 (tp30) cc_final: 0.6706 (tt0) REVERT: D 293 HIS cc_start: 0.7438 (m-70) cc_final: 0.6299 (t-90) REVERT: D 325 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7472 (tp30) REVERT: D 329 LYS cc_start: 0.7772 (mttt) cc_final: 0.7303 (mtpm) REVERT: D 352 ASP cc_start: 0.7869 (m-30) cc_final: 0.7482 (m-30) REVERT: D 353 LYS cc_start: 0.6725 (ttpp) cc_final: 0.6491 (tptp) REVERT: D 367 LYS cc_start: 0.8310 (tttt) cc_final: 0.7895 (tttm) REVERT: D 380 TYR cc_start: 0.7583 (m-80) cc_final: 0.7043 (m-80) REVERT: D 409 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7404 (mtt) REVERT: D 435 LYS cc_start: 0.7508 (mttm) cc_final: 0.7307 (mttm) REVERT: D 477 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8000 (mt-10) outliers start: 46 outliers final: 10 residues processed: 329 average time/residue: 1.1839 time to fit residues: 431.3473 Evaluate side-chains 288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 270 time to evaluate : 1.551 ------------------------------------------------------------------------------- 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 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 88 optimal weight: 0.7980 chunk 182 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.3554 r_free = 0.3554 target = 0.142377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.113779 restraints weight = 15325.601| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.38 r_work: 0.3131 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15496 Z= 0.266 Angle : 0.634 7.532 20984 Z= 0.339 Chirality : 0.049 0.173 2324 Planarity : 0.005 0.034 2716 Dihedral : 5.243 23.706 2104 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.73 % Allowed : 18.67 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 1964 helix: 0.94 (0.18), residues: 832 sheet: 0.16 (0.26), residues: 408 loop : 0.09 (0.22), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 178 HIS 0.006 0.002 HIS B 236 PHE 0.016 0.003 PHE B 483 TYR 0.017 0.003 TYR B 154 ARG 0.003 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04586 ( 720) hydrogen bonds : angle 5.40269 ( 2100) covalent geometry : bond 0.00640 (15496) covalent geometry : angle 0.63396 (20984) *********************** 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 316 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 272 time to evaluate : 1.545 Fit side-chains REVERT: A 31 ASP cc_start: 0.7363 (m-30) cc_final: 0.7002 (p0) REVERT: A 53 GLU cc_start: 0.8262 (mm-30) cc_final: 0.7664 (mm-30) REVERT: A 57 LYS cc_start: 0.7857 (tttm) cc_final: 0.7496 (tttp) REVERT: A 84 GLU cc_start: 0.7508 (tp30) cc_final: 0.7118 (mp0) REVERT: A 98 ARG cc_start: 0.8063 (ttp-170) cc_final: 0.7854 (ttp-170) REVERT: A 107 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5730 (mm-30) REVERT: A 109 MET cc_start: 0.7981 (mtp) cc_final: 0.7741 (mtm) REVERT: A 240 ASP cc_start: 0.7962 (m-30) cc_final: 0.7616 (m-30) REVERT: A 269 GLU cc_start: 0.7286 (tp30) cc_final: 0.6992 (tt0) REVERT: A 293 HIS cc_start: 0.7540 (m-70) cc_final: 0.6390 (t-90) REVERT: A 313 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6713 (pm20) REVERT: A 325 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7547 (tp30) REVERT: A 329 LYS cc_start: 0.7680 (mttt) cc_final: 0.7305 (mtpm) REVERT: A 352 ASP cc_start: 0.7915 (m-30) cc_final: 0.7526 (m-30) REVERT: A 353 LYS cc_start: 0.6821 (ttpp) cc_final: 0.6449 (tptp) REVERT: A 357 LEU cc_start: 0.7218 (mt) cc_final: 0.6836 (mt) REVERT: A 367 LYS cc_start: 0.8360 (tttt) cc_final: 0.7996 (tttm) REVERT: A 380 TYR cc_start: 0.7623 (m-80) cc_final: 0.7141 (m-80) REVERT: A 409 MET cc_start: 0.8272 (OUTLIER) cc_final: 0.7340 (mtt) REVERT: A 412 LYS cc_start: 0.7621 (mtmt) cc_final: 0.7403 (mtpt) REVERT: A 416 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: B 31 ASP cc_start: 0.7369 (m-30) cc_final: 0.7003 (p0) REVERT: B 53 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7691 (mm-30) REVERT: B 57 LYS cc_start: 0.7866 (tttm) cc_final: 0.7506 (tttp) REVERT: B 84 GLU cc_start: 0.7433 (tp30) cc_final: 0.7088 (mp0) REVERT: B 98 ARG cc_start: 0.8052 (ttp-170) cc_final: 0.7667 (ttm170) REVERT: B 107 GLU cc_start: 0.6998 (OUTLIER) cc_final: 0.5779 (mm-30) REVERT: B 109 MET cc_start: 0.7984 (mtp) cc_final: 0.7743 (mtm) REVERT: B 240 ASP cc_start: 0.7974 (m-30) cc_final: 0.7627 (m-30) REVERT: B 269 GLU cc_start: 0.7298 (tp30) cc_final: 0.7008 (tt0) REVERT: B 293 HIS cc_start: 0.7511 (m-70) cc_final: 0.6366 (t-90) REVERT: B 313 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: B 325 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7559 (tp30) REVERT: B 329 LYS cc_start: 0.7671 (mttt) cc_final: 0.7290 (mtpm) REVERT: B 352 ASP cc_start: 0.7911 (m-30) cc_final: 0.7518 (m-30) REVERT: B 353 LYS cc_start: 0.6834 (ttpp) cc_final: 0.6452 (tptp) REVERT: B 357 LEU cc_start: 0.7222 (mt) cc_final: 0.6841 (mt) REVERT: B 367 LYS cc_start: 0.8376 (tttt) cc_final: 0.8015 (tttm) REVERT: B 380 TYR cc_start: 0.7625 (m-80) cc_final: 0.7145 (m-80) REVERT: B 409 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: B 416 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7232 (m-30) REVERT: C 31 ASP cc_start: 0.7369 (m-30) cc_final: 0.7009 (p0) REVERT: C 53 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7769 (mm-30) REVERT: C 57 LYS cc_start: 0.7848 (tttm) cc_final: 0.7491 (tttp) REVERT: C 69 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7786 (tm-30) REVERT: C 84 GLU cc_start: 0.7488 (tp30) cc_final: 0.7109 (mp0) REVERT: C 98 ARG cc_start: 0.8023 (ttp-170) cc_final: 0.7808 (ttp-170) REVERT: C 107 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.5733 (mm-30) REVERT: C 109 MET cc_start: 0.7977 (mtp) cc_final: 0.7734 (mtm) REVERT: C 240 ASP cc_start: 0.7940 (m-30) cc_final: 0.7624 (m-30) REVERT: C 269 GLU cc_start: 0.7289 (tp30) cc_final: 0.6995 (tt0) REVERT: C 293 HIS cc_start: 0.7517 (m-70) cc_final: 0.6380 (t-90) REVERT: C 325 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7543 (tp30) REVERT: C 329 LYS cc_start: 0.7655 (mttt) cc_final: 0.7281 (mtpm) REVERT: C 352 ASP cc_start: 0.7884 (m-30) cc_final: 0.7488 (m-30) REVERT: C 353 LYS cc_start: 0.6813 (ttpp) cc_final: 0.6436 (tptp) REVERT: C 357 LEU cc_start: 0.7213 (mt) cc_final: 0.6828 (mt) REVERT: C 367 LYS cc_start: 0.8374 (tttt) cc_final: 0.8018 (tttm) REVERT: C 380 TYR cc_start: 0.7625 (m-80) cc_final: 0.7191 (m-80) REVERT: C 409 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7368 (mtt) REVERT: C 416 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7220 (m-30) REVERT: C 435 LYS cc_start: 0.7674 (mttm) cc_final: 0.7406 (mttm) REVERT: D 31 ASP cc_start: 0.7355 (m-30) cc_final: 0.7004 (p0) REVERT: D 53 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7768 (mm-30) REVERT: D 57 LYS cc_start: 0.7839 (tttm) cc_final: 0.7482 (tttp) REVERT: D 69 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7782 (tm-30) REVERT: D 84 GLU cc_start: 0.7399 (tp30) cc_final: 0.7097 (mp0) REVERT: D 98 ARG cc_start: 0.8040 (ttp-170) cc_final: 0.7665 (ttm170) REVERT: D 107 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.5751 (mm-30) REVERT: D 109 MET cc_start: 0.7976 (mtp) cc_final: 0.7734 (mtm) REVERT: D 240 ASP cc_start: 0.7937 (m-30) cc_final: 0.7619 (m-30) REVERT: D 269 GLU cc_start: 0.7293 (tp30) cc_final: 0.6999 (tt0) REVERT: D 293 HIS cc_start: 0.7510 (m-70) cc_final: 0.6371 (t-90) REVERT: D 325 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7540 (tp30) REVERT: D 329 LYS cc_start: 0.7667 (mttt) cc_final: 0.7295 (mtpm) REVERT: D 352 ASP cc_start: 0.7905 (m-30) cc_final: 0.7510 (m-30) REVERT: D 353 LYS cc_start: 0.6821 (ttpp) cc_final: 0.6450 (tptp) REVERT: D 357 LEU cc_start: 0.7235 (mt) cc_final: 0.6856 (mt) REVERT: D 367 LYS cc_start: 0.8373 (tttt) cc_final: 0.8013 (tttm) REVERT: D 380 TYR cc_start: 0.7620 (m-80) cc_final: 0.7192 (m-80) REVERT: D 409 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7360 (mtt) REVERT: D 416 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7195 (m-30) REVERT: D 435 LYS cc_start: 0.7681 (mttm) cc_final: 0.7405 (mttm) outliers start: 44 outliers final: 12 residues processed: 298 average time/residue: 1.3184 time to fit residues: 431.3856 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 416 ASP 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 416 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 47 optimal weight: 1.9990 chunk 141 optimal weight: 0.9990 chunk 143 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN B 117 ASN B 220 ASN C 117 ASN D 117 ASN D 220 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.145312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118721 restraints weight = 15520.339| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.27 r_work: 0.3163 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15496 Z= 0.130 Angle : 0.504 6.687 20984 Z= 0.269 Chirality : 0.043 0.139 2324 Planarity : 0.004 0.030 2716 Dihedral : 4.785 20.887 2104 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.60 % Allowed : 19.73 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.19), residues: 1964 helix: 1.61 (0.18), residues: 800 sheet: 0.19 (0.26), residues: 408 loop : 0.11 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 453 HIS 0.003 0.001 HIS B 30 PHE 0.008 0.001 PHE D 483 TYR 0.015 0.002 TYR B 351 ARG 0.001 0.000 ARG B 326 Details of bonding type rmsd hydrogen bonds : bond 0.03470 ( 720) hydrogen bonds : angle 5.11096 ( 2100) covalent geometry : bond 0.00304 (15496) covalent geometry : angle 0.50434 (20984) *********************** 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 331 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 1.564 Fit side-chains REVERT: A 31 ASP cc_start: 0.7370 (m-30) cc_final: 0.7011 (p0) REVERT: A 53 GLU cc_start: 0.8162 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 57 LYS cc_start: 0.7758 (tttm) cc_final: 0.7361 (tttp) REVERT: A 84 GLU cc_start: 0.7409 (tp30) cc_final: 0.6950 (mm-30) REVERT: A 98 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7597 (ttm170) REVERT: A 107 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.6240 (tp30) REVERT: A 220 ASN cc_start: 0.8874 (OUTLIER) cc_final: 0.8619 (m110) REVERT: A 240 ASP cc_start: 0.7904 (m-30) cc_final: 0.7550 (m-30) REVERT: A 293 HIS cc_start: 0.7422 (m-70) cc_final: 0.6299 (t-90) REVERT: A 313 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6725 (pm20) REVERT: A 325 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7550 (tp30) REVERT: A 329 LYS cc_start: 0.7662 (mttt) cc_final: 0.7204 (mtpm) REVERT: A 352 ASP cc_start: 0.7840 (m-30) cc_final: 0.7490 (m-30) REVERT: A 353 LYS cc_start: 0.6804 (ttpp) cc_final: 0.6436 (tptp) REVERT: A 357 LEU cc_start: 0.7261 (mt) cc_final: 0.6879 (mt) REVERT: A 367 LYS cc_start: 0.8329 (tttt) cc_final: 0.7961 (tttm) REVERT: A 380 TYR cc_start: 0.7539 (m-80) cc_final: 0.7031 (m-80) REVERT: A 409 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7225 (mtt) REVERT: A 412 LYS cc_start: 0.7608 (mtmt) cc_final: 0.7394 (mtpt) REVERT: A 416 ASP cc_start: 0.7628 (m-30) cc_final: 0.7138 (m-30) REVERT: A 435 LYS cc_start: 0.7461 (mttm) cc_final: 0.7249 (mttm) REVERT: B 31 ASP cc_start: 0.7365 (m-30) cc_final: 0.7008 (p0) REVERT: B 53 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7600 (mm-30) REVERT: B 57 LYS cc_start: 0.7754 (tttm) cc_final: 0.7353 (tttp) REVERT: B 84 GLU cc_start: 0.7377 (tp30) cc_final: 0.6933 (mm-30) REVERT: B 98 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7582 (ttm170) REVERT: B 107 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6289 (tp30) REVERT: B 220 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8669 (m-40) REVERT: B 240 ASP cc_start: 0.7919 (m-30) cc_final: 0.7565 (m-30) REVERT: B 293 HIS cc_start: 0.7399 (m-70) cc_final: 0.6289 (t-90) REVERT: B 325 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7576 (tp30) REVERT: B 329 LYS cc_start: 0.7668 (mttt) cc_final: 0.7204 (mtpm) REVERT: B 352 ASP cc_start: 0.7841 (m-30) cc_final: 0.7488 (m-30) REVERT: B 353 LYS cc_start: 0.6812 (ttpp) cc_final: 0.6439 (tptp) REVERT: B 357 LEU cc_start: 0.7275 (mt) cc_final: 0.6891 (mt) REVERT: B 367 LYS cc_start: 0.8330 (tttt) cc_final: 0.7964 (tttm) REVERT: B 380 TYR cc_start: 0.7532 (m-80) cc_final: 0.7020 (m-80) REVERT: B 409 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7217 (mtt) REVERT: B 416 ASP cc_start: 0.7621 (m-30) cc_final: 0.7173 (m-30) REVERT: B 435 LYS cc_start: 0.7464 (mttm) cc_final: 0.7250 (mttm) REVERT: C 31 ASP cc_start: 0.7352 (m-30) cc_final: 0.6994 (p0) REVERT: C 53 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7603 (mm-30) REVERT: C 54 GLU cc_start: 0.7693 (tp30) cc_final: 0.7078 (tp30) REVERT: C 57 LYS cc_start: 0.7746 (tttm) cc_final: 0.7371 (tttp) REVERT: C 84 GLU cc_start: 0.7389 (tp30) cc_final: 0.6934 (mm-30) REVERT: C 98 ARG cc_start: 0.7989 (ttp-170) cc_final: 0.7560 (ttm170) REVERT: C 107 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.6272 (tp30) REVERT: C 220 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8557 (m110) REVERT: C 240 ASP cc_start: 0.7881 (m-30) cc_final: 0.7582 (m-30) REVERT: C 293 HIS cc_start: 0.7409 (m-70) cc_final: 0.6304 (t-90) REVERT: C 325 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7560 (tp30) REVERT: C 329 LYS cc_start: 0.7663 (mttt) cc_final: 0.7198 (mtpm) REVERT: C 352 ASP cc_start: 0.7821 (m-30) cc_final: 0.7467 (m-30) REVERT: C 353 LYS cc_start: 0.6801 (ttpp) cc_final: 0.6436 (tptp) REVERT: C 357 LEU cc_start: 0.7264 (mt) cc_final: 0.6877 (mt) REVERT: C 367 LYS cc_start: 0.8337 (tttt) cc_final: 0.7973 (tttm) REVERT: C 380 TYR cc_start: 0.7551 (m-80) cc_final: 0.7028 (m-80) REVERT: C 416 ASP cc_start: 0.7622 (OUTLIER) cc_final: 0.7177 (m-30) REVERT: C 435 LYS cc_start: 0.7369 (mttm) cc_final: 0.7065 (mttm) REVERT: D 31 ASP cc_start: 0.7335 (m-30) cc_final: 0.6992 (p0) REVERT: D 53 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7608 (mm-30) REVERT: D 54 GLU cc_start: 0.7707 (tp30) cc_final: 0.7099 (tp30) REVERT: D 57 LYS cc_start: 0.7746 (tttm) cc_final: 0.7374 (tttp) REVERT: D 84 GLU cc_start: 0.7382 (tp30) cc_final: 0.6933 (mm-30) REVERT: D 98 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7578 (ttm170) REVERT: D 107 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6269 (tp30) REVERT: D 220 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8630 (m-40) REVERT: D 240 ASP cc_start: 0.7872 (m-30) cc_final: 0.7574 (m-30) REVERT: D 293 HIS cc_start: 0.7407 (m-70) cc_final: 0.6289 (t-90) REVERT: D 325 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7577 (tp30) REVERT: D 329 LYS cc_start: 0.7678 (mttt) cc_final: 0.7230 (mtpm) REVERT: D 352 ASP cc_start: 0.7841 (m-30) cc_final: 0.7491 (m-30) REVERT: D 353 LYS cc_start: 0.6806 (ttpp) cc_final: 0.6441 (tptp) REVERT: D 357 LEU cc_start: 0.7282 (mt) cc_final: 0.6898 (mt) REVERT: D 367 LYS cc_start: 0.8345 (tttt) cc_final: 0.7979 (tttm) REVERT: D 380 TYR cc_start: 0.7536 (m-80) cc_final: 0.7015 (m-80) REVERT: D 416 ASP cc_start: 0.7615 (m-30) cc_final: 0.7164 (m-30) REVERT: D 435 LYS cc_start: 0.7429 (mttm) cc_final: 0.7138 (mttm) outliers start: 58 outliers final: 10 residues processed: 318 average time/residue: 1.2104 time to fit residues: 426.0247 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 253 time to evaluate : 1.654 ------------------------------------------------------------------------------- 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 220 ASN 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 220 ASN Chi-restraints excluded: chain B residue 409 MET 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 220 ASN Chi-restraints excluded: chain C residue 416 ASP 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 220 ASN 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 28 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 118 optimal weight: 0.0270 chunk 179 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 117 ASN B 110 ASN B 117 ASN B 220 ASN C 110 ASN C 117 ASN C 455 ASN D 110 ASN D 117 ASN D 220 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.143273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.117017 restraints weight = 15534.584| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.27 r_work: 0.3136 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 15496 Z= 0.232 Angle : 0.592 7.475 20984 Z= 0.316 Chirality : 0.049 0.369 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.958 21.923 2104 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.78 % Allowed : 19.17 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1964 helix: 1.35 (0.18), residues: 804 sheet: 0.16 (0.26), residues: 408 loop : -0.00 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 136 HIS 0.004 0.002 HIS D 236 PHE 0.013 0.002 PHE D 483 TYR 0.022 0.003 TYR B 351 ARG 0.003 0.000 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 720) hydrogen bonds : angle 5.23877 ( 2100) covalent geometry : bond 0.00563 (15496) covalent geometry : angle 0.59227 (20984) *********************** 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 320 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 1.542 Fit side-chains REVERT: A 31 ASP cc_start: 0.7386 (m-30) cc_final: 0.7024 (p0) REVERT: A 53 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 57 LYS cc_start: 0.7803 (tttm) cc_final: 0.7446 (tttp) REVERT: A 84 GLU cc_start: 0.7447 (tp30) cc_final: 0.7157 (mp0) REVERT: A 107 GLU cc_start: 0.6909 (OUTLIER) cc_final: 0.5712 (mm-30) REVERT: A 240 ASP cc_start: 0.7908 (m-30) cc_final: 0.7586 (m-30) REVERT: A 293 HIS cc_start: 0.7484 (m-70) cc_final: 0.6354 (t-90) REVERT: A 313 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: A 325 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7462 (tp30) REVERT: A 329 LYS cc_start: 0.7507 (mttt) cc_final: 0.7133 (mtpm) REVERT: A 352 ASP cc_start: 0.7833 (m-30) cc_final: 0.7487 (m-30) REVERT: A 353 LYS cc_start: 0.6886 (ttpp) cc_final: 0.6476 (tptp) REVERT: A 357 LEU cc_start: 0.7297 (mt) cc_final: 0.6884 (mt) REVERT: A 367 LYS cc_start: 0.8362 (tttt) cc_final: 0.8001 (tttm) REVERT: A 380 TYR cc_start: 0.7585 (m-80) cc_final: 0.7107 (m-80) REVERT: A 409 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7300 (mtt) REVERT: A 416 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.6988 (m-30) REVERT: A 435 LYS cc_start: 0.7556 (mttm) cc_final: 0.7288 (mttm) REVERT: A 481 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: B 31 ASP cc_start: 0.7373 (m-30) cc_final: 0.7018 (p0) REVERT: B 53 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7604 (mm-30) REVERT: B 57 LYS cc_start: 0.7794 (tttm) cc_final: 0.7438 (tttp) REVERT: B 84 GLU cc_start: 0.7418 (tp30) cc_final: 0.7075 (mm-30) REVERT: B 107 GLU cc_start: 0.6930 (OUTLIER) cc_final: 0.5735 (mm-30) REVERT: B 240 ASP cc_start: 0.7914 (m-30) cc_final: 0.7589 (m-30) REVERT: B 293 HIS cc_start: 0.7475 (m-70) cc_final: 0.6340 (t-90) REVERT: B 325 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7489 (tp30) REVERT: B 329 LYS cc_start: 0.7512 (mttt) cc_final: 0.7129 (mtpm) REVERT: B 352 ASP cc_start: 0.7839 (m-30) cc_final: 0.7493 (m-30) REVERT: B 353 LYS cc_start: 0.6906 (ttpp) cc_final: 0.6506 (tptp) REVERT: B 357 LEU cc_start: 0.7302 (mt) cc_final: 0.6935 (mt) REVERT: B 367 LYS cc_start: 0.8358 (tttt) cc_final: 0.7996 (tttm) REVERT: B 380 TYR cc_start: 0.7591 (m-80) cc_final: 0.7114 (m-80) REVERT: B 409 MET cc_start: 0.8256 (OUTLIER) cc_final: 0.7254 (mtt) REVERT: B 416 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7030 (m-30) REVERT: B 435 LYS cc_start: 0.7555 (mttm) cc_final: 0.7286 (mttm) REVERT: B 481 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.6155 (m-80) REVERT: C 31 ASP cc_start: 0.7376 (m-30) cc_final: 0.7019 (p0) REVERT: C 53 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7620 (mm-30) REVERT: C 54 GLU cc_start: 0.7665 (tp30) cc_final: 0.7271 (tp30) REVERT: C 57 LYS cc_start: 0.7778 (tttm) cc_final: 0.7461 (tttp) REVERT: C 84 GLU cc_start: 0.7430 (tp30) cc_final: 0.7137 (mp0) REVERT: C 107 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.5722 (mm-30) REVERT: C 220 ASN cc_start: 0.8859 (OUTLIER) cc_final: 0.8584 (m110) REVERT: C 240 ASP cc_start: 0.7920 (m-30) cc_final: 0.7607 (m-30) REVERT: C 293 HIS cc_start: 0.7479 (m-70) cc_final: 0.6364 (t-90) REVERT: C 325 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7470 (tp30) REVERT: C 329 LYS cc_start: 0.7501 (mttt) cc_final: 0.7124 (mtpm) REVERT: C 352 ASP cc_start: 0.7834 (m-30) cc_final: 0.7490 (m-30) REVERT: C 353 LYS cc_start: 0.6898 (ttpp) cc_final: 0.6498 (tptp) REVERT: C 357 LEU cc_start: 0.7268 (mt) cc_final: 0.6891 (mt) REVERT: C 367 LYS cc_start: 0.8358 (tttt) cc_final: 0.8003 (tttm) REVERT: C 380 TYR cc_start: 0.7584 (m-80) cc_final: 0.7103 (m-80) REVERT: C 409 MET cc_start: 0.8247 (OUTLIER) cc_final: 0.7220 (mtm) REVERT: C 416 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7203 (m-30) REVERT: C 435 LYS cc_start: 0.7565 (mttm) cc_final: 0.7329 (mttm) REVERT: C 481 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: D 31 ASP cc_start: 0.7368 (m-30) cc_final: 0.7015 (p0) REVERT: D 53 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7618 (mm-30) REVERT: D 54 GLU cc_start: 0.7675 (tp30) cc_final: 0.7290 (tp30) REVERT: D 57 LYS cc_start: 0.7774 (tttm) cc_final: 0.7463 (tttp) REVERT: D 84 GLU cc_start: 0.7416 (tp30) cc_final: 0.7090 (mm-30) REVERT: D 107 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.5719 (mm-30) REVERT: D 240 ASP cc_start: 0.7897 (m-30) cc_final: 0.7587 (m-30) REVERT: D 293 HIS cc_start: 0.7474 (m-70) cc_final: 0.6340 (t-90) REVERT: D 325 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7493 (tp30) REVERT: D 329 LYS cc_start: 0.7511 (mttt) cc_final: 0.7136 (mtpm) REVERT: D 352 ASP cc_start: 0.7841 (m-30) cc_final: 0.7497 (m-30) REVERT: D 353 LYS cc_start: 0.6893 (ttpp) cc_final: 0.6491 (tptp) REVERT: D 357 LEU cc_start: 0.7286 (mt) cc_final: 0.6919 (mt) REVERT: D 367 LYS cc_start: 0.8368 (tttt) cc_final: 0.8012 (tttm) REVERT: D 380 TYR cc_start: 0.7581 (m-80) cc_final: 0.7105 (m-80) REVERT: D 409 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7265 (mtm) REVERT: D 416 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7166 (m-30) REVERT: D 435 LYS cc_start: 0.7566 (mttm) cc_final: 0.7329 (mttm) REVERT: D 481 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6154 (m-80) outliers start: 61 outliers final: 24 residues processed: 295 average time/residue: 1.1701 time to fit residues: 382.3517 Evaluate side-chains 292 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 250 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 266 VAL Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 409 MET Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR 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 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 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 416 ASP Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 481 TYR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 185 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 455 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 = 0.3599 r_free = 0.3599 target = 0.146003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.120068 restraints weight = 15515.740| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.32 r_work: 0.3179 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3758 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= 0.123 Angle : 0.498 6.700 20984 Z= 0.265 Chirality : 0.044 0.279 2324 Planarity : 0.004 0.031 2716 Dihedral : 4.629 19.824 2104 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.41 % Allowed : 19.48 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 1964 helix: 1.68 (0.18), residues: 800 sheet: 0.14 (0.27), residues: 384 loop : 0.10 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 453 HIS 0.003 0.001 HIS A 30 PHE 0.011 0.001 PHE D 38 TYR 0.018 0.002 TYR C 351 ARG 0.001 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 720) hydrogen bonds : angle 5.02078 ( 2100) covalent geometry : bond 0.00291 (15496) covalent geometry : angle 0.49817 (20984) *********************** 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 321 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 266 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7491 (m-30) cc_final: 0.7117 (p0) REVERT: A 53 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7615 (mm-30) REVERT: A 57 LYS cc_start: 0.7697 (tttm) cc_final: 0.7286 (ttmt) REVERT: A 84 GLU cc_start: 0.7419 (tp30) cc_final: 0.6985 (mm-30) REVERT: A 107 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6341 (tp30) REVERT: A 220 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8660 (m-40) REVERT: A 240 ASP cc_start: 0.7984 (m-30) cc_final: 0.7664 (m-30) REVERT: A 293 HIS cc_start: 0.7379 (m-70) cc_final: 0.6245 (t-90) REVERT: A 325 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7566 (tp30) REVERT: A 329 LYS cc_start: 0.7534 (mttt) cc_final: 0.7081 (mtpm) REVERT: A 353 LYS cc_start: 0.6821 (ttpp) cc_final: 0.6399 (tptt) REVERT: A 357 LEU cc_start: 0.7258 (mt) cc_final: 0.6825 (mt) REVERT: A 367 LYS cc_start: 0.8323 (tttt) cc_final: 0.7974 (tttm) REVERT: A 380 TYR cc_start: 0.7455 (m-80) cc_final: 0.6922 (m-80) REVERT: A 435 LYS cc_start: 0.7451 (mttm) cc_final: 0.7232 (mttm) REVERT: A 481 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6120 (m-80) REVERT: B 31 ASP cc_start: 0.7484 (m-30) cc_final: 0.7113 (p0) REVERT: B 53 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7588 (mm-30) REVERT: B 57 LYS cc_start: 0.7677 (tttm) cc_final: 0.7262 (ttmt) REVERT: B 84 GLU cc_start: 0.7416 (tp30) cc_final: 0.6989 (mm-30) REVERT: B 107 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6394 (tp30) REVERT: B 240 ASP cc_start: 0.7980 (m-30) cc_final: 0.7656 (m-30) REVERT: B 293 HIS cc_start: 0.7365 (m-70) cc_final: 0.6225 (t-90) REVERT: B 325 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7530 (tp30) REVERT: B 329 LYS cc_start: 0.7533 (mttt) cc_final: 0.7071 (mtpm) REVERT: B 352 ASP cc_start: 0.7805 (m-30) cc_final: 0.7465 (m-30) REVERT: B 353 LYS cc_start: 0.6829 (ttpp) cc_final: 0.6400 (tptt) REVERT: B 357 LEU cc_start: 0.7265 (mt) cc_final: 0.6832 (mt) REVERT: B 367 LYS cc_start: 0.8325 (tttt) cc_final: 0.7972 (tttm) REVERT: B 380 TYR cc_start: 0.7448 (m-80) cc_final: 0.6913 (m-80) REVERT: B 435 LYS cc_start: 0.7432 (mttm) cc_final: 0.7216 (mttm) REVERT: B 481 TYR cc_start: 0.7042 (OUTLIER) cc_final: 0.6136 (m-80) REVERT: C 31 ASP cc_start: 0.7444 (m-30) cc_final: 0.7075 (p0) REVERT: C 53 GLU cc_start: 0.8245 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 54 GLU cc_start: 0.7624 (tp30) cc_final: 0.6951 (tp30) REVERT: C 57 LYS cc_start: 0.7716 (tttm) cc_final: 0.7298 (tttt) REVERT: C 84 GLU cc_start: 0.7394 (tp30) cc_final: 0.6965 (mm-30) REVERT: C 107 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6373 (tp30) REVERT: C 220 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8569 (m110) REVERT: C 240 ASP cc_start: 0.7976 (m-30) cc_final: 0.7674 (m-30) REVERT: C 293 HIS cc_start: 0.7367 (m-70) cc_final: 0.6245 (t-90) REVERT: C 325 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7493 (tp30) REVERT: C 329 LYS cc_start: 0.7505 (mttt) cc_final: 0.7054 (mtpm) REVERT: C 353 LYS cc_start: 0.6815 (ttpp) cc_final: 0.6399 (tptt) REVERT: C 357 LEU cc_start: 0.7254 (mt) cc_final: 0.6820 (mt) REVERT: C 367 LYS cc_start: 0.8331 (tttt) cc_final: 0.7993 (tttm) REVERT: C 380 TYR cc_start: 0.7439 (m-80) cc_final: 0.6901 (m-80) REVERT: C 409 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7150 (mtm) REVERT: C 435 LYS cc_start: 0.7364 (mttm) cc_final: 0.7060 (mttm) REVERT: C 481 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.6154 (m-80) REVERT: D 31 ASP cc_start: 0.7451 (m-30) cc_final: 0.7084 (p0) REVERT: D 53 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7623 (mm-30) REVERT: D 54 GLU cc_start: 0.7630 (tp30) cc_final: 0.6960 (tp30) REVERT: D 57 LYS cc_start: 0.7713 (tttm) cc_final: 0.7299 (tttt) REVERT: D 84 GLU cc_start: 0.7401 (tp30) cc_final: 0.6992 (mm-30) REVERT: D 107 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.6360 (tp30) REVERT: D 240 ASP cc_start: 0.7975 (m-30) cc_final: 0.7673 (m-30) REVERT: D 293 HIS cc_start: 0.7368 (m-70) cc_final: 0.6219 (t-90) REVERT: D 325 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7543 (tp30) REVERT: D 329 LYS cc_start: 0.7528 (mttt) cc_final: 0.7076 (mtpm) REVERT: D 352 ASP cc_start: 0.7800 (m-30) cc_final: 0.7459 (m-30) REVERT: D 353 LYS cc_start: 0.6818 (ttpp) cc_final: 0.6397 (tptt) REVERT: D 357 LEU cc_start: 0.7282 (mt) cc_final: 0.6850 (mt) REVERT: D 367 LYS cc_start: 0.8333 (tttt) cc_final: 0.7990 (tttm) REVERT: D 380 TYR cc_start: 0.7427 (m-80) cc_final: 0.6890 (m-80) REVERT: D 409 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7152 (mtm) REVERT: D 435 LYS cc_start: 0.7344 (mttm) cc_final: 0.7050 (mttm) REVERT: D 481 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.6140 (m-80) outliers start: 55 outliers final: 18 residues processed: 299 average time/residue: 1.1902 time to fit residues: 394.2511 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 244 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 481 TYR 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 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 220 ASN Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 416 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.3980 chunk 167 optimal weight: 0.0040 chunk 178 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 150 optimal weight: 0.0070 chunk 98 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.8012 ------------------------------------------------------------------------------- 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 C 19 GLN D 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.146348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.119794 restraints weight = 15564.609| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.33 r_work: 0.3182 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15496 Z= 0.127 Angle : 0.501 6.722 20984 Z= 0.267 Chirality : 0.044 0.258 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.551 19.423 2104 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.29 % Allowed : 20.72 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 1964 helix: 1.70 (0.18), residues: 804 sheet: 0.15 (0.26), residues: 404 loop : 0.14 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 178 HIS 0.002 0.001 HIS B 30 PHE 0.010 0.001 PHE D 38 TYR 0.019 0.002 TYR D 351 ARG 0.002 0.000 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.03329 ( 720) hydrogen bonds : angle 4.93639 ( 2100) covalent geometry : bond 0.00300 (15496) covalent geometry : angle 0.50110 (20984) *********************** 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 306 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 253 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7469 (m-30) cc_final: 0.7030 (p0) REVERT: A 53 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 57 LYS cc_start: 0.7685 (tttm) cc_final: 0.7263 (ttmt) REVERT: A 84 GLU cc_start: 0.7382 (tp30) cc_final: 0.6935 (mm-30) REVERT: A 107 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6331 (tp30) REVERT: A 109 MET cc_start: 0.7818 (mtm) cc_final: 0.7603 (mtm) REVERT: A 220 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8476 (m110) REVERT: A 240 ASP cc_start: 0.7994 (m-30) cc_final: 0.7646 (m-30) REVERT: A 293 HIS cc_start: 0.7368 (m-70) cc_final: 0.6230 (t-90) REVERT: A 325 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7499 (tp30) REVERT: A 329 LYS cc_start: 0.7449 (mttt) cc_final: 0.7095 (mtpm) REVERT: A 353 LYS cc_start: 0.6802 (ttpp) cc_final: 0.6376 (tptt) REVERT: A 357 LEU cc_start: 0.7237 (mt) cc_final: 0.6794 (mt) REVERT: A 367 LYS cc_start: 0.8299 (tttt) cc_final: 0.7951 (tttm) REVERT: A 380 TYR cc_start: 0.7394 (m-80) cc_final: 0.6933 (m-80) REVERT: A 409 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7232 (mtt) REVERT: A 435 LYS cc_start: 0.7390 (mttm) cc_final: 0.7166 (mttm) REVERT: A 481 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6106 (m-80) REVERT: B 31 ASP cc_start: 0.7474 (m-30) cc_final: 0.7039 (p0) REVERT: B 53 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 57 LYS cc_start: 0.7678 (tttm) cc_final: 0.7250 (ttmt) REVERT: B 84 GLU cc_start: 0.7411 (tp30) cc_final: 0.6979 (mm-30) REVERT: B 107 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6354 (tp30) REVERT: B 109 MET cc_start: 0.7822 (mtm) cc_final: 0.7608 (mtm) REVERT: B 240 ASP cc_start: 0.7994 (m-30) cc_final: 0.7648 (m-30) REVERT: B 293 HIS cc_start: 0.7364 (m-70) cc_final: 0.6236 (t-90) REVERT: B 325 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7507 (tp30) REVERT: B 329 LYS cc_start: 0.7468 (mttt) cc_final: 0.7095 (mtpm) REVERT: B 352 ASP cc_start: 0.7781 (m-30) cc_final: 0.7442 (m-30) REVERT: B 353 LYS cc_start: 0.6808 (ttpp) cc_final: 0.6392 (tptt) REVERT: B 357 LEU cc_start: 0.7252 (mt) cc_final: 0.6810 (mt) REVERT: B 367 LYS cc_start: 0.8308 (tttt) cc_final: 0.7957 (tttm) REVERT: B 380 TYR cc_start: 0.7377 (m-80) cc_final: 0.6912 (m-80) REVERT: B 435 LYS cc_start: 0.7403 (mttm) cc_final: 0.7184 (mttm) REVERT: B 481 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6110 (m-80) REVERT: C 31 ASP cc_start: 0.7478 (m-30) cc_final: 0.7046 (p0) REVERT: C 53 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 54 GLU cc_start: 0.7623 (tp30) cc_final: 0.6938 (tp30) REVERT: C 57 LYS cc_start: 0.7692 (tttm) cc_final: 0.7285 (tttt) REVERT: C 84 GLU cc_start: 0.7393 (tp30) cc_final: 0.6931 (mm-30) REVERT: C 107 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6350 (tp30) REVERT: C 109 MET cc_start: 0.7836 (mtm) cc_final: 0.7623 (mtm) REVERT: C 220 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8566 (m110) REVERT: C 240 ASP cc_start: 0.7947 (m-30) cc_final: 0.7651 (m-30) REVERT: C 293 HIS cc_start: 0.7361 (m-70) cc_final: 0.6240 (t-90) REVERT: C 325 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7481 (tp30) REVERT: C 329 LYS cc_start: 0.7454 (mttt) cc_final: 0.7091 (mtpm) REVERT: C 353 LYS cc_start: 0.6808 (ttpp) cc_final: 0.6410 (tptt) REVERT: C 357 LEU cc_start: 0.7239 (mt) cc_final: 0.6838 (mt) REVERT: C 367 LYS cc_start: 0.8309 (tttt) cc_final: 0.7971 (tttm) REVERT: C 380 TYR cc_start: 0.7393 (m-80) cc_final: 0.6928 (m-80) REVERT: C 409 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7123 (mtm) REVERT: C 435 LYS cc_start: 0.7303 (mttm) cc_final: 0.6956 (mttm) REVERT: C 481 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.6141 (m-80) REVERT: D 31 ASP cc_start: 0.7459 (m-30) cc_final: 0.7041 (p0) REVERT: D 53 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7602 (mm-30) REVERT: D 54 GLU cc_start: 0.7628 (tp30) cc_final: 0.7264 (tp30) REVERT: D 57 LYS cc_start: 0.7691 (tttm) cc_final: 0.7288 (tttt) REVERT: D 84 GLU cc_start: 0.7407 (tp30) cc_final: 0.6976 (mm-30) REVERT: D 107 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6331 (tp30) REVERT: D 109 MET cc_start: 0.7847 (mtm) cc_final: 0.7636 (mtm) REVERT: D 240 ASP cc_start: 0.7963 (m-30) cc_final: 0.7643 (m-30) REVERT: D 293 HIS cc_start: 0.7323 (m-70) cc_final: 0.6191 (t-90) REVERT: D 325 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7454 (tp30) REVERT: D 329 LYS cc_start: 0.7464 (mttt) cc_final: 0.7105 (mtpm) REVERT: D 352 ASP cc_start: 0.7778 (m-30) cc_final: 0.7440 (m-30) REVERT: D 353 LYS cc_start: 0.6811 (ttpp) cc_final: 0.6411 (tptt) REVERT: D 357 LEU cc_start: 0.7267 (mt) cc_final: 0.6867 (mt) REVERT: D 367 LYS cc_start: 0.8316 (tttt) cc_final: 0.7969 (tttm) REVERT: D 380 TYR cc_start: 0.7372 (m-80) cc_final: 0.6899 (m-80) REVERT: D 409 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7102 (mtm) REVERT: D 435 LYS cc_start: 0.7319 (mttm) cc_final: 0.6890 (mttm) REVERT: D 481 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6119 (m-80) outliers start: 53 outliers final: 20 residues processed: 287 average time/residue: 1.2101 time to fit residues: 383.8683 Evaluate side-chains 272 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 409 MET Chi-restraints excluded: chain A residue 416 ASP 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 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 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 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 174 optimal weight: 3.9990 chunk 183 optimal weight: 8.9990 chunk 167 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 chunk 108 optimal weight: 8.9990 chunk 153 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 C 19 GLN D 19 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.145881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119646 restraints weight = 15379.981| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.31 r_work: 0.3179 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15496 Z= 0.150 Angle : 0.520 6.955 20984 Z= 0.277 Chirality : 0.045 0.251 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.595 19.304 2104 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.92 % Allowed : 20.41 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 1964 helix: 1.65 (0.18), residues: 804 sheet: 0.16 (0.26), residues: 404 loop : 0.12 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 178 HIS 0.003 0.001 HIS B 30 PHE 0.011 0.002 PHE D 38 TYR 0.020 0.002 TYR A 351 ARG 0.002 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 720) hydrogen bonds : angle 4.96667 ( 2100) covalent geometry : bond 0.00361 (15496) covalent geometry : angle 0.51969 (20984) *********************** 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 296 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7464 (m-30) cc_final: 0.7033 (p0) REVERT: A 53 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 57 LYS cc_start: 0.7745 (tttm) cc_final: 0.7364 (tttt) REVERT: A 84 GLU cc_start: 0.7406 (tp30) cc_final: 0.7008 (mm-30) REVERT: A 107 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6344 (tp30) REVERT: A 220 ASN cc_start: 0.8711 (OUTLIER) cc_final: 0.8500 (m110) REVERT: A 240 ASP cc_start: 0.7999 (m-30) cc_final: 0.7634 (m-30) REVERT: A 293 HIS cc_start: 0.7364 (m-70) cc_final: 0.6242 (t-90) REVERT: A 325 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7524 (tp30) REVERT: A 329 LYS cc_start: 0.7488 (mttt) cc_final: 0.7095 (mtpm) REVERT: A 353 LYS cc_start: 0.6817 (ttpp) cc_final: 0.6406 (tptt) REVERT: A 357 LEU cc_start: 0.7261 (mt) cc_final: 0.6856 (mt) REVERT: A 367 LYS cc_start: 0.8308 (tttt) cc_final: 0.7963 (tttm) REVERT: A 380 TYR cc_start: 0.7373 (m-80) cc_final: 0.6893 (m-80) REVERT: A 409 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7275 (mtt) REVERT: A 435 LYS cc_start: 0.7443 (mttm) cc_final: 0.7215 (mttm) REVERT: A 481 TYR cc_start: 0.7019 (OUTLIER) cc_final: 0.6125 (m-80) REVERT: B 31 ASP cc_start: 0.7467 (m-30) cc_final: 0.7041 (p0) REVERT: B 53 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7583 (mm-30) REVERT: B 57 LYS cc_start: 0.7726 (tttm) cc_final: 0.7348 (tttt) REVERT: B 84 GLU cc_start: 0.7411 (tp30) cc_final: 0.7026 (mm-30) REVERT: B 107 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6375 (tp30) REVERT: B 240 ASP cc_start: 0.7996 (m-30) cc_final: 0.7634 (m-30) REVERT: B 293 HIS cc_start: 0.7351 (m-70) cc_final: 0.6245 (t-90) REVERT: B 325 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7498 (tp30) REVERT: B 329 LYS cc_start: 0.7487 (mttt) cc_final: 0.7092 (mtpm) REVERT: B 352 ASP cc_start: 0.7792 (m-30) cc_final: 0.7457 (m-30) REVERT: B 353 LYS cc_start: 0.6818 (ttpp) cc_final: 0.6416 (tptt) REVERT: B 357 LEU cc_start: 0.7277 (mt) cc_final: 0.6877 (mt) REVERT: B 367 LYS cc_start: 0.8338 (tttt) cc_final: 0.7999 (tttm) REVERT: B 380 TYR cc_start: 0.7358 (m-80) cc_final: 0.6876 (m-80) REVERT: B 409 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7175 (mtm) REVERT: B 435 LYS cc_start: 0.7434 (mttm) cc_final: 0.7214 (mttm) REVERT: B 481 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: C 31 ASP cc_start: 0.7486 (m-30) cc_final: 0.7057 (p0) REVERT: C 53 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7632 (mm-30) REVERT: C 54 GLU cc_start: 0.7615 (tp30) cc_final: 0.7234 (tp30) REVERT: C 57 LYS cc_start: 0.7762 (tttm) cc_final: 0.7363 (tttt) REVERT: C 84 GLU cc_start: 0.7407 (tp30) cc_final: 0.7004 (mm-30) REVERT: C 107 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.6337 (tp30) REVERT: C 240 ASP cc_start: 0.7979 (m-30) cc_final: 0.7636 (m-30) REVERT: C 293 HIS cc_start: 0.7363 (m-70) cc_final: 0.6262 (t-90) REVERT: C 325 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7496 (tp30) REVERT: C 329 LYS cc_start: 0.7484 (mttt) cc_final: 0.7095 (mtpm) REVERT: C 353 LYS cc_start: 0.6824 (ttpp) cc_final: 0.6414 (tptt) REVERT: C 357 LEU cc_start: 0.7240 (mt) cc_final: 0.6814 (mt) REVERT: C 367 LYS cc_start: 0.8342 (tttt) cc_final: 0.8006 (tttm) REVERT: C 380 TYR cc_start: 0.7378 (m-80) cc_final: 0.6899 (m-80) REVERT: C 409 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7130 (mtm) REVERT: C 481 TYR cc_start: 0.7023 (OUTLIER) cc_final: 0.6137 (m-80) REVERT: D 31 ASP cc_start: 0.7477 (m-30) cc_final: 0.7049 (p0) REVERT: D 53 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7620 (mm-30) REVERT: D 54 GLU cc_start: 0.7635 (tp30) cc_final: 0.7257 (tp30) REVERT: D 57 LYS cc_start: 0.7750 (tttm) cc_final: 0.7352 (tttt) REVERT: D 84 GLU cc_start: 0.7403 (tp30) cc_final: 0.7037 (mm-30) REVERT: D 107 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: D 240 ASP cc_start: 0.7986 (m-30) cc_final: 0.7646 (m-30) REVERT: D 293 HIS cc_start: 0.7355 (m-70) cc_final: 0.6239 (t-90) REVERT: D 325 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7512 (tp30) REVERT: D 329 LYS cc_start: 0.7503 (mttt) cc_final: 0.7118 (mtpm) REVERT: D 352 ASP cc_start: 0.7796 (m-30) cc_final: 0.7458 (m-30) REVERT: D 353 LYS cc_start: 0.6820 (ttpp) cc_final: 0.6412 (tptt) REVERT: D 357 LEU cc_start: 0.7274 (mt) cc_final: 0.6853 (mt) REVERT: D 367 LYS cc_start: 0.8342 (tttt) cc_final: 0.8001 (tttm) REVERT: D 380 TYR cc_start: 0.7381 (m-80) cc_final: 0.6896 (m-80) REVERT: D 409 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7115 (mtm) REVERT: D 435 LYS cc_start: 0.7343 (mttm) cc_final: 0.7082 (mttm) REVERT: D 481 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6123 (m-80) outliers start: 47 outliers final: 24 residues processed: 280 average time/residue: 1.2516 time to fit residues: 388.4810 Evaluate side-chains 281 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 244 time to evaluate : 1.560 ------------------------------------------------------------------------------- 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 416 ASP 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 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 266 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 416 ASP 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 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 116 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 186 optimal weight: 0.7980 chunk 187 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 176 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 C 19 GLN C 220 ASN D 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.146355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.119881 restraints weight = 15598.081| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.25 r_work: 0.3188 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3853 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= 0.124 Angle : 0.503 6.684 20984 Z= 0.268 Chirality : 0.044 0.241 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.516 18.739 2104 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.30 % Allowed : 21.71 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 1964 helix: 1.65 (0.18), residues: 804 sheet: 0.31 (0.27), residues: 376 loop : 0.12 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 178 HIS 0.002 0.001 HIS B 30 PHE 0.010 0.001 PHE D 38 TYR 0.018 0.002 TYR B 351 ARG 0.003 0.000 ARG B 131 Details of bonding type rmsd hydrogen bonds : bond 0.03299 ( 720) hydrogen bonds : angle 4.94146 ( 2100) covalent geometry : bond 0.00296 (15496) covalent geometry : angle 0.50272 (20984) ********************** 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 292 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 255 time to evaluate : 1.810 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7458 (m-30) cc_final: 0.7032 (p0) REVERT: A 53 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7609 (mm-30) REVERT: A 57 LYS cc_start: 0.7699 (tttm) cc_final: 0.7334 (tttt) REVERT: A 84 GLU cc_start: 0.7355 (tp30) cc_final: 0.6942 (mm-30) REVERT: A 107 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: A 220 ASN cc_start: 0.8788 (OUTLIER) cc_final: 0.8549 (m110) REVERT: A 240 ASP cc_start: 0.7954 (m-30) cc_final: 0.7586 (m-30) REVERT: A 293 HIS cc_start: 0.7299 (m-70) cc_final: 0.6208 (t-90) REVERT: A 325 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7557 (tp30) REVERT: A 329 LYS cc_start: 0.7436 (mttt) cc_final: 0.7067 (mtpm) REVERT: A 353 LYS cc_start: 0.6824 (ttpp) cc_final: 0.6416 (tptt) REVERT: A 357 LEU cc_start: 0.7233 (mt) cc_final: 0.6786 (mt) REVERT: A 367 LYS cc_start: 0.8320 (tttt) cc_final: 0.8007 (tttm) REVERT: A 380 TYR cc_start: 0.7322 (m-80) cc_final: 0.6826 (m-80) REVERT: A 409 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7212 (mtt) REVERT: A 435 LYS cc_start: 0.7357 (mttm) cc_final: 0.7070 (mttm) REVERT: A 481 TYR cc_start: 0.6966 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: B 31 ASP cc_start: 0.7456 (m-30) cc_final: 0.7033 (p0) REVERT: B 53 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 57 LYS cc_start: 0.7692 (tttm) cc_final: 0.7316 (tttt) REVERT: B 84 GLU cc_start: 0.7362 (tp30) cc_final: 0.6948 (mm-30) REVERT: B 107 GLU cc_start: 0.6805 (OUTLIER) cc_final: 0.6326 (tp30) REVERT: B 240 ASP cc_start: 0.7961 (m-30) cc_final: 0.7604 (m-30) REVERT: B 293 HIS cc_start: 0.7313 (m-70) cc_final: 0.6242 (t-90) REVERT: B 325 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7530 (tp30) REVERT: B 329 LYS cc_start: 0.7433 (mttt) cc_final: 0.7059 (mtpm) REVERT: B 352 ASP cc_start: 0.7811 (m-30) cc_final: 0.7479 (m-30) REVERT: B 353 LYS cc_start: 0.6817 (ttpp) cc_final: 0.6411 (tptt) REVERT: B 357 LEU cc_start: 0.7246 (mt) cc_final: 0.6801 (mt) REVERT: B 367 LYS cc_start: 0.8326 (tttt) cc_final: 0.8015 (tttm) REVERT: B 380 TYR cc_start: 0.7317 (m-80) cc_final: 0.6820 (m-80) REVERT: B 416 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.6926 (m-30) REVERT: B 435 LYS cc_start: 0.7350 (mttm) cc_final: 0.7062 (mttm) REVERT: B 481 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: C 31 ASP cc_start: 0.7487 (m-30) cc_final: 0.7064 (p0) REVERT: C 53 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7654 (mm-30) REVERT: C 54 GLU cc_start: 0.7580 (tp30) cc_final: 0.7198 (tp30) REVERT: C 57 LYS cc_start: 0.7727 (tttm) cc_final: 0.7330 (tttt) REVERT: C 84 GLU cc_start: 0.7362 (tp30) cc_final: 0.6936 (mm-30) REVERT: C 107 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6333 (tp30) REVERT: C 220 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8496 (m110) REVERT: C 240 ASP cc_start: 0.7941 (m-30) cc_final: 0.7601 (m-30) REVERT: C 293 HIS cc_start: 0.7308 (m-70) cc_final: 0.6237 (t-90) REVERT: C 325 GLU cc_start: 0.7828 (mm-30) cc_final: 0.7529 (tp30) REVERT: C 329 LYS cc_start: 0.7434 (mttt) cc_final: 0.7059 (mtpm) REVERT: C 353 LYS cc_start: 0.6847 (ttpp) cc_final: 0.6452 (tptt) REVERT: C 357 LEU cc_start: 0.7247 (mt) cc_final: 0.6799 (mt) REVERT: C 367 LYS cc_start: 0.8334 (tttt) cc_final: 0.8032 (tttm) REVERT: C 380 TYR cc_start: 0.7311 (m-80) cc_final: 0.6860 (m-80) REVERT: C 409 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7097 (mtm) REVERT: C 416 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.6986 (m-30) REVERT: C 481 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6103 (m-80) REVERT: D 31 ASP cc_start: 0.7469 (m-30) cc_final: 0.7051 (p0) REVERT: D 53 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7654 (mm-30) REVERT: D 54 GLU cc_start: 0.7657 (tp30) cc_final: 0.7289 (tp30) REVERT: D 57 LYS cc_start: 0.7734 (tttm) cc_final: 0.7338 (tttt) REVERT: D 84 GLU cc_start: 0.7341 (tp30) cc_final: 0.6942 (mm-30) REVERT: D 107 GLU cc_start: 0.6799 (OUTLIER) cc_final: 0.6319 (tp30) REVERT: D 240 ASP cc_start: 0.7952 (m-30) cc_final: 0.7613 (m-30) REVERT: D 293 HIS cc_start: 0.7311 (m-70) cc_final: 0.6224 (t-90) REVERT: D 325 GLU cc_start: 0.7822 (mm-30) cc_final: 0.7520 (tp30) REVERT: D 329 LYS cc_start: 0.7437 (mttt) cc_final: 0.7070 (mtpm) REVERT: D 352 ASP cc_start: 0.7814 (m-30) cc_final: 0.7485 (m-30) REVERT: D 353 LYS cc_start: 0.6835 (ttpp) cc_final: 0.6422 (tptt) REVERT: D 357 LEU cc_start: 0.7260 (mt) cc_final: 0.6811 (mt) REVERT: D 367 LYS cc_start: 0.8327 (tttt) cc_final: 0.8020 (tttm) REVERT: D 380 TYR cc_start: 0.7308 (m-80) cc_final: 0.6860 (m-80) REVERT: D 409 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7103 (mtm) REVERT: D 416 ASP cc_start: 0.7589 (OUTLIER) cc_final: 0.6966 (m-30) REVERT: D 481 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6092 (m-80) outliers start: 37 outliers final: 21 residues processed: 277 average time/residue: 1.2134 time to fit residues: 372.3877 Evaluate side-chains 275 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 238 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 416 ASP 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 266 VAL 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 416 ASP 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 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 45 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 157 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 C 19 GLN C 220 ASN D 19 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.143809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115867 restraints weight = 15723.106| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.38 r_work: 0.3139 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15496 Z= 0.228 Angle : 0.590 7.489 20984 Z= 0.314 Chirality : 0.048 0.305 2324 Planarity : 0.005 0.033 2716 Dihedral : 4.773 20.182 2104 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.67 % Allowed : 21.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1964 helix: 1.49 (0.18), residues: 804 sheet: 0.28 (0.27), residues: 384 loop : 0.03 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 136 HIS 0.004 0.001 HIS B 30 PHE 0.012 0.002 PHE B 483 TYR 0.023 0.003 TYR C 351 ARG 0.003 0.001 ARG C 326 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 720) hydrogen bonds : angle 5.08416 ( 2100) covalent geometry : bond 0.00555 (15496) covalent geometry : angle 0.58981 (20984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11183.88 seconds wall clock time: 193 minutes 11.29 seconds (11591.29 seconds total)