Starting phenix.real_space_refine on Fri Jun 13 17:21:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pvh_17966/06_2025/8pvh_17966.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pvh_17966/06_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_17966/06_2025/8pvh_17966.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pvh_17966/06_2025/8pvh_17966.map" model { file = "/net/cci-nas-00/data/ceres_data/8pvh_17966/06_2025/8pvh_17966.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pvh_17966/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.36, per 1000 atoms: 0.55 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: 3.70 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: 2.16 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: 5.59 Time building geometry restraints manager: 4.44 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: 0.12 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: 2.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 37.210 Find NCS groups from input model: 0.330 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:15.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.320 ------------------------------------------------------------------------------- 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 : 1.673 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: 1.5165 time to fit residues: 803.7478 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 : 1.634 ------------------------------------------------------------------------------- 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 = 0.149287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.120488 restraints weight = 14814.873| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.30 r_work: 0.3203 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2241 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 6.459 20984 Z= 0.313 Chirality : 0.046 0.235 2324 Planarity : 0.004 0.035 2716 Dihedral : 5.292 18.730 2120 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.03 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 5.39754 ( 2100) covalent geometry : bond 0.00301 (15496) covalent geometry : angle 0.56994 (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 : 1.583 Fit side-chains REVERT: A 31 ASP cc_start: 0.7390 (m-30) cc_final: 0.7064 (p0) REVERT: A 53 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 57 LYS cc_start: 0.7798 (tttm) cc_final: 0.7417 (tttp) REVERT: A 84 GLU cc_start: 0.7572 (tp30) cc_final: 0.7050 (mm-30) REVERT: A 98 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7627 (ttp-170) REVERT: A 107 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.5743 (mm-30) REVERT: A 117 ASN cc_start: 0.7925 (m-40) cc_final: 0.7524 (m-40) REVERT: A 119 TYR cc_start: 0.8306 (t80) cc_final: 0.7874 (t80) REVERT: A 158 GLU cc_start: 0.7611 (mt-10) cc_final: 0.7261 (tt0) REVERT: A 193 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8137 (tmmt) REVERT: A 240 ASP cc_start: 0.7960 (m-30) cc_final: 0.7642 (m-30) REVERT: A 253 LEU cc_start: 0.8152 (mt) cc_final: 0.7864 (mm) REVERT: A 293 HIS cc_start: 0.7441 (m-70) cc_final: 0.6335 (t-90) REVERT: A 295 VAL cc_start: 0.8232 (p) cc_final: 0.7757 (t) REVERT: A 325 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7619 (tp30) REVERT: A 329 LYS cc_start: 0.7749 (mttt) cc_final: 0.7307 (mtpm) REVERT: A 357 LEU cc_start: 0.7330 (mt) cc_final: 0.6729 (mt) REVERT: A 367 LYS cc_start: 0.8308 (tttt) cc_final: 0.7899 (tttm) REVERT: A 380 TYR cc_start: 0.7515 (m-80) cc_final: 0.6892 (m-80) REVERT: A 416 ASP cc_start: 0.6660 (t70) cc_final: 0.6352 (t0) REVERT: A 442 THR cc_start: 0.8438 (m) cc_final: 0.8145 (m) REVERT: B 31 ASP cc_start: 0.7385 (m-30) cc_final: 0.7054 (p0) REVERT: B 53 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7839 (mm-30) REVERT: B 57 LYS cc_start: 0.7807 (tttm) cc_final: 0.7430 (tttp) REVERT: B 84 GLU cc_start: 0.7551 (tp30) cc_final: 0.7037 (mm-30) REVERT: B 98 ARG cc_start: 0.7926 (ttp-170) cc_final: 0.7620 (ttp-170) REVERT: B 107 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5759 (mm-30) REVERT: B 117 ASN cc_start: 0.7905 (m-40) cc_final: 0.7516 (m-40) REVERT: B 119 TYR cc_start: 0.8298 (t80) cc_final: 0.7868 (t80) REVERT: B 158 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7265 (tt0) REVERT: B 193 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8142 (tmmt) REVERT: B 240 ASP cc_start: 0.7963 (m-30) cc_final: 0.7645 (m-30) REVERT: B 253 LEU cc_start: 0.8169 (mt) cc_final: 0.7882 (mm) REVERT: B 293 HIS cc_start: 0.7441 (m-70) cc_final: 0.6336 (t-90) REVERT: B 295 VAL cc_start: 0.8228 (p) cc_final: 0.7758 (t) REVERT: B 325 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7596 (tp30) REVERT: B 329 LYS cc_start: 0.7753 (mttt) cc_final: 0.7309 (mtpm) REVERT: B 352 ASP cc_start: 0.7607 (m-30) cc_final: 0.7250 (m-30) REVERT: B 357 LEU cc_start: 0.7310 (mt) cc_final: 0.6704 (mt) REVERT: B 367 LYS cc_start: 0.8298 (tttt) cc_final: 0.7884 (tttm) REVERT: B 380 TYR cc_start: 0.7516 (m-80) cc_final: 0.6903 (m-80) REVERT: B 416 ASP cc_start: 0.6654 (t70) cc_final: 0.6348 (t0) REVERT: B 442 THR cc_start: 0.8447 (m) cc_final: 0.8150 (m) REVERT: C 31 ASP cc_start: 0.7393 (m-30) cc_final: 0.7069 (p0) REVERT: C 53 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7856 (mm-30) REVERT: C 57 LYS cc_start: 0.7789 (tttm) cc_final: 0.7419 (tttp) REVERT: C 84 GLU cc_start: 0.7583 (tp30) cc_final: 0.7047 (mm-30) REVERT: C 98 ARG cc_start: 0.7941 (ttp-170) cc_final: 0.7628 (ttp-170) REVERT: C 107 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.5752 (mm-30) REVERT: C 117 ASN cc_start: 0.7922 (m-40) cc_final: 0.7516 (m-40) REVERT: C 119 TYR cc_start: 0.8298 (t80) cc_final: 0.7864 (t80) REVERT: C 158 GLU cc_start: 0.7615 (mt-10) cc_final: 0.7262 (tt0) REVERT: C 240 ASP cc_start: 0.7952 (m-30) cc_final: 0.7631 (m-30) REVERT: C 253 LEU cc_start: 0.8153 (mt) cc_final: 0.7868 (mm) REVERT: C 293 HIS cc_start: 0.7442 (m-70) cc_final: 0.6331 (t-90) REVERT: C 295 VAL cc_start: 0.8229 (p) cc_final: 0.7755 (t) REVERT: C 325 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7605 (tp30) REVERT: C 329 LYS cc_start: 0.7751 (mttt) cc_final: 0.7311 (mtpm) REVERT: C 357 LEU cc_start: 0.7306 (mt) cc_final: 0.6709 (mt) REVERT: C 367 LYS cc_start: 0.8295 (tttt) cc_final: 0.7879 (tttm) REVERT: C 380 TYR cc_start: 0.7513 (m-80) cc_final: 0.6888 (m-80) REVERT: C 416 ASP cc_start: 0.6680 (t70) cc_final: 0.6368 (t0) REVERT: C 436 ASP cc_start: 0.7421 (t70) cc_final: 0.7220 (t0) REVERT: C 442 THR cc_start: 0.8441 (m) cc_final: 0.8144 (m) REVERT: D 31 ASP cc_start: 0.7414 (m-30) cc_final: 0.7073 (p0) REVERT: D 53 GLU cc_start: 0.8282 (mm-30) cc_final: 0.7848 (mm-30) REVERT: D 57 LYS cc_start: 0.7804 (tttm) cc_final: 0.7431 (tttp) REVERT: D 84 GLU cc_start: 0.7548 (tp30) cc_final: 0.7020 (mm-30) REVERT: D 98 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7621 (ttp-170) REVERT: D 107 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.5761 (mm-30) REVERT: D 117 ASN cc_start: 0.7915 (m-40) cc_final: 0.7518 (m-40) REVERT: D 119 TYR cc_start: 0.8297 (t80) cc_final: 0.7868 (t80) REVERT: D 158 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7261 (tt0) REVERT: D 193 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.8142 (tmmt) REVERT: D 240 ASP cc_start: 0.7946 (m-30) cc_final: 0.7632 (m-30) REVERT: D 253 LEU cc_start: 0.8170 (mt) cc_final: 0.7888 (mm) REVERT: D 293 HIS cc_start: 0.7437 (m-70) cc_final: 0.6323 (t-90) REVERT: D 295 VAL cc_start: 0.8226 (p) cc_final: 0.7756 (t) REVERT: D 325 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7594 (tp30) REVERT: D 329 LYS cc_start: 0.7746 (mttt) cc_final: 0.7300 (mtpm) REVERT: D 352 ASP cc_start: 0.7609 (m-30) cc_final: 0.7254 (m-30) REVERT: D 357 LEU cc_start: 0.7318 (mt) cc_final: 0.6723 (mt) REVERT: D 367 LYS cc_start: 0.8318 (tttt) cc_final: 0.7913 (tttm) REVERT: D 380 TYR cc_start: 0.7496 (m-80) cc_final: 0.6873 (m-80) REVERT: D 416 ASP cc_start: 0.6687 (t70) cc_final: 0.6373 (t0) REVERT: D 436 ASP cc_start: 0.7422 (t70) cc_final: 0.7220 (t0) REVERT: D 442 THR cc_start: 0.8455 (m) cc_final: 0.8157 (m) outliers start: 47 outliers final: 4 residues processed: 359 average time/residue: 1.2830 time to fit residues: 506.6329 Evaluate side-chains 265 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 254 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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: 0.0020 chunk 169 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 0.4980 chunk 20 optimal weight: 0.0270 overall best weight: 0.4846 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.151089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121955 restraints weight = 14979.917| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.34 r_work: 0.3206 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15496 Z= 0.108 Angle : 0.499 6.300 20984 Z= 0.268 Chirality : 0.044 0.158 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.678 18.759 2104 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.23 % Allowed : 17.87 % Favored : 79.90 % 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: 1.26 (0.19), residues: 1964 helix: 1.67 (0.18), residues: 800 sheet: 0.33 (0.25), residues: 416 loop : 0.38 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 178 HIS 0.003 0.001 HIS D 236 PHE 0.007 0.001 PHE C 310 TYR 0.014 0.001 TYR C 20 ARG 0.006 0.000 ARG A 321 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 720) hydrogen bonds : angle 5.01927 ( 2100) covalent geometry : bond 0.00233 (15496) covalent geometry : angle 0.49930 (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 334 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 298 time to evaluate : 1.815 Fit side-chains REVERT: A 31 ASP cc_start: 0.7384 (m-30) cc_final: 0.7053 (p0) REVERT: A 53 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 57 LYS cc_start: 0.7769 (tttm) cc_final: 0.7290 (ttmt) REVERT: A 84 GLU cc_start: 0.7320 (tp30) cc_final: 0.6951 (mm-30) REVERT: A 98 ARG cc_start: 0.7954 (ttp-170) cc_final: 0.7616 (ttp-170) REVERT: A 107 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5967 (mm-30) REVERT: A 117 ASN cc_start: 0.8007 (m-40) cc_final: 0.7646 (m-40) REVERT: A 138 ASP cc_start: 0.8231 (p0) cc_final: 0.7947 (p0) REVERT: A 158 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7331 (tt0) REVERT: A 240 ASP cc_start: 0.7825 (m-30) cc_final: 0.7551 (m-30) REVERT: A 293 HIS cc_start: 0.7370 (m-70) cc_final: 0.6281 (t-90) REVERT: A 325 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7448 (tp30) REVERT: A 329 LYS cc_start: 0.7752 (mttt) cc_final: 0.7266 (mtpm) REVERT: A 352 ASP cc_start: 0.7859 (m-30) cc_final: 0.7476 (m-30) REVERT: A 357 LEU cc_start: 0.7216 (mt) cc_final: 0.6775 (mt) REVERT: A 367 LYS cc_start: 0.8359 (tttt) cc_final: 0.7960 (tttm) REVERT: A 380 TYR cc_start: 0.7546 (m-80) cc_final: 0.7002 (m-80) REVERT: A 435 LYS cc_start: 0.7270 (mttm) cc_final: 0.7031 (mttm) REVERT: A 442 THR cc_start: 0.8492 (m) cc_final: 0.8172 (m) REVERT: B 31 ASP cc_start: 0.7367 (m-30) cc_final: 0.7045 (p0) REVERT: B 53 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7866 (mm-30) REVERT: B 57 LYS cc_start: 0.7768 (tttm) cc_final: 0.7295 (ttmt) REVERT: B 84 GLU cc_start: 0.7341 (tp30) cc_final: 0.6940 (mm-30) REVERT: B 98 ARG cc_start: 0.7943 (ttp-170) cc_final: 0.7606 (ttp-170) REVERT: B 107 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5977 (mm-30) REVERT: B 117 ASN cc_start: 0.8025 (m-40) cc_final: 0.7662 (m-40) REVERT: B 138 ASP cc_start: 0.8259 (p0) cc_final: 0.7979 (p0) REVERT: B 158 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7312 (tt0) REVERT: B 240 ASP cc_start: 0.7845 (m-30) cc_final: 0.7580 (m-30) REVERT: B 293 HIS cc_start: 0.7366 (m-70) cc_final: 0.6276 (t-90) REVERT: B 325 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7484 (tp30) REVERT: B 329 LYS cc_start: 0.7745 (mttt) cc_final: 0.7262 (mtpm) REVERT: B 352 ASP cc_start: 0.7837 (m-30) cc_final: 0.7450 (m-30) REVERT: B 357 LEU cc_start: 0.7193 (mt) cc_final: 0.6749 (mt) REVERT: B 367 LYS cc_start: 0.8342 (tttt) cc_final: 0.7940 (tttm) REVERT: B 380 TYR cc_start: 0.7529 (m-80) cc_final: 0.6973 (m-80) REVERT: B 435 LYS cc_start: 0.7254 (mttm) cc_final: 0.7010 (mttm) REVERT: B 442 THR cc_start: 0.8485 (m) cc_final: 0.8156 (m) REVERT: C 31 ASP cc_start: 0.7392 (m-30) cc_final: 0.7055 (p0) REVERT: C 53 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7853 (mm-30) REVERT: C 57 LYS cc_start: 0.7757 (tttm) cc_final: 0.7282 (ttmt) REVERT: C 84 GLU cc_start: 0.7326 (tp30) cc_final: 0.6952 (mm-30) REVERT: C 98 ARG cc_start: 0.7929 (ttp-170) cc_final: 0.7590 (ttp-170) REVERT: C 107 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.5967 (mm-30) REVERT: C 117 ASN cc_start: 0.8017 (m-40) cc_final: 0.7662 (m-40) REVERT: C 158 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7305 (tt0) REVERT: C 240 ASP cc_start: 0.7849 (m-30) cc_final: 0.7576 (m-30) REVERT: C 253 LEU cc_start: 0.8221 (mt) cc_final: 0.7925 (mm) REVERT: C 293 HIS cc_start: 0.7361 (m-70) cc_final: 0.6268 (t-90) REVERT: C 325 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7477 (tp30) REVERT: C 329 LYS cc_start: 0.7755 (mttt) cc_final: 0.7264 (mtpm) REVERT: C 352 ASP cc_start: 0.7853 (m-30) cc_final: 0.7468 (m-30) REVERT: C 357 LEU cc_start: 0.7217 (mt) cc_final: 0.6771 (mt) REVERT: C 367 LYS cc_start: 0.8363 (tttt) cc_final: 0.7964 (tttm) REVERT: C 435 LYS cc_start: 0.7291 (mttm) cc_final: 0.7078 (mttm) REVERT: C 442 THR cc_start: 0.8541 (m) cc_final: 0.8199 (m) REVERT: D 31 ASP cc_start: 0.7404 (m-30) cc_final: 0.7054 (p0) REVERT: D 53 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7840 (mm-30) REVERT: D 57 LYS cc_start: 0.7771 (tttm) cc_final: 0.7295 (ttmt) REVERT: D 84 GLU cc_start: 0.7330 (tp30) cc_final: 0.6938 (mm-30) REVERT: D 98 ARG cc_start: 0.7944 (ttp-170) cc_final: 0.7607 (ttp-170) REVERT: D 107 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6002 (mm-30) REVERT: D 117 ASN cc_start: 0.8013 (m-40) cc_final: 0.7645 (m-40) REVERT: D 138 ASP cc_start: 0.8229 (p0) cc_final: 0.7975 (p0) REVERT: D 158 GLU cc_start: 0.7649 (mt-10) cc_final: 0.7309 (tt0) REVERT: D 240 ASP cc_start: 0.7866 (m-30) cc_final: 0.7592 (m-30) REVERT: D 253 LEU cc_start: 0.8204 (mt) cc_final: 0.7904 (mm) REVERT: D 293 HIS cc_start: 0.7348 (m-70) cc_final: 0.6265 (t-90) REVERT: D 325 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7471 (tp30) REVERT: D 329 LYS cc_start: 0.7753 (mttt) cc_final: 0.7265 (mtpm) REVERT: D 352 ASP cc_start: 0.7859 (m-30) cc_final: 0.7476 (m-30) REVERT: D 357 LEU cc_start: 0.7203 (mt) cc_final: 0.6755 (mt) REVERT: D 367 LYS cc_start: 0.8343 (tttt) cc_final: 0.7940 (tttm) REVERT: D 435 LYS cc_start: 0.7261 (mttm) cc_final: 0.7044 (mttm) REVERT: D 442 THR cc_start: 0.8528 (m) cc_final: 0.8183 (m) outliers start: 36 outliers final: 12 residues processed: 326 average time/residue: 1.2079 time to fit residues: 436.4520 Evaluate side-chains 289 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 273 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 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 464 CYS Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 88 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 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: 2.9990 chunk 102 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 195 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.142599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.114127 restraints weight = 15306.008| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.36 r_work: 0.3131 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 15496 Z= 0.285 Angle : 0.643 7.441 20984 Z= 0.344 Chirality : 0.050 0.153 2324 Planarity : 0.005 0.037 2716 Dihedral : 5.226 23.357 2104 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.10 % Allowed : 17.74 % Favored : 79.16 % 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: 0.67 (0.19), residues: 1964 helix: 0.94 (0.17), residues: 832 sheet: 0.26 (0.26), residues: 408 loop : 0.18 (0.23), 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 C 483 TYR 0.016 0.003 TYR A 154 ARG 0.004 0.001 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.04663 ( 720) hydrogen bonds : angle 5.38437 ( 2100) covalent geometry : bond 0.00688 (15496) covalent geometry : angle 0.64333 (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 318 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 268 time to evaluate : 1.771 Fit side-chains REVERT: A 31 ASP cc_start: 0.7366 (m-30) cc_final: 0.7010 (p0) REVERT: A 53 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7751 (mm-30) REVERT: A 57 LYS cc_start: 0.7883 (tttm) cc_final: 0.7494 (tttp) REVERT: A 69 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7798 (tm-30) REVERT: A 84 GLU cc_start: 0.7478 (tp30) cc_final: 0.6942 (mm-30) REVERT: A 98 ARG cc_start: 0.8074 (ttp-170) cc_final: 0.7864 (ttp-170) REVERT: A 107 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.5704 (mm-30) REVERT: A 109 MET cc_start: 0.7972 (mtp) cc_final: 0.7770 (mtm) REVERT: A 117 ASN cc_start: 0.8190 (m-40) cc_final: 0.7803 (m-40) REVERT: A 240 ASP cc_start: 0.7944 (m-30) cc_final: 0.7585 (m-30) REVERT: A 293 HIS cc_start: 0.7506 (m-70) cc_final: 0.6383 (t-90) REVERT: A 313 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6716 (pm20) REVERT: A 325 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7490 (tp30) REVERT: A 329 LYS cc_start: 0.7737 (mttt) cc_final: 0.7311 (mtpm) REVERT: A 352 ASP cc_start: 0.7863 (m-30) cc_final: 0.7482 (m-30) REVERT: A 353 LYS cc_start: 0.6785 (ttpp) cc_final: 0.6435 (tptp) REVERT: A 357 LEU cc_start: 0.7327 (mt) cc_final: 0.6870 (mt) REVERT: A 367 LYS cc_start: 0.8366 (tttt) cc_final: 0.7999 (tttm) REVERT: A 380 TYR cc_start: 0.7609 (m-80) cc_final: 0.7143 (m-80) REVERT: A 409 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7359 (mtt) REVERT: A 412 LYS cc_start: 0.7641 (mtmt) cc_final: 0.7402 (mtpt) REVERT: A 416 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: A 435 LYS cc_start: 0.7706 (mttm) cc_final: 0.7503 (mttm) REVERT: B 31 ASP cc_start: 0.7364 (m-30) cc_final: 0.7010 (p0) REVERT: B 53 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 57 LYS cc_start: 0.7887 (tttm) cc_final: 0.7497 (tttp) REVERT: B 69 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7791 (tm-30) REVERT: B 84 GLU cc_start: 0.7478 (tp30) cc_final: 0.6932 (mm-30) REVERT: B 98 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7848 (ttp-170) REVERT: B 107 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.5732 (mm-30) REVERT: B 109 MET cc_start: 0.7979 (mtp) cc_final: 0.7775 (mtm) REVERT: B 117 ASN cc_start: 0.8184 (m-40) cc_final: 0.7797 (m-40) REVERT: B 240 ASP cc_start: 0.7942 (m-30) cc_final: 0.7585 (m-30) REVERT: B 293 HIS cc_start: 0.7496 (m-70) cc_final: 0.6348 (t-90) REVERT: B 313 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: B 325 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7509 (tp30) REVERT: B 329 LYS cc_start: 0.7730 (mttt) cc_final: 0.7298 (mtpm) REVERT: B 352 ASP cc_start: 0.7863 (m-30) cc_final: 0.7479 (m-30) REVERT: B 353 LYS cc_start: 0.6796 (ttpp) cc_final: 0.6435 (tptp) REVERT: B 357 LEU cc_start: 0.7318 (mt) cc_final: 0.6864 (mt) REVERT: B 367 LYS cc_start: 0.8368 (tttt) cc_final: 0.8000 (tttm) REVERT: B 380 TYR cc_start: 0.7611 (m-80) cc_final: 0.7145 (m-80) REVERT: B 409 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7348 (mtt) REVERT: B 412 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7407 (mtpt) REVERT: B 416 ASP cc_start: 0.7698 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: B 435 LYS cc_start: 0.7690 (mttm) cc_final: 0.7488 (mttm) REVERT: C 31 ASP cc_start: 0.7370 (m-30) cc_final: 0.7016 (p0) REVERT: C 53 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7768 (mm-30) REVERT: C 57 LYS cc_start: 0.7872 (tttm) cc_final: 0.7487 (tttp) REVERT: C 69 GLN cc_start: 0.8016 (tp-100) cc_final: 0.7810 (tm-30) REVERT: C 84 GLU cc_start: 0.7481 (tp30) cc_final: 0.6947 (mm-30) REVERT: C 98 ARG cc_start: 0.8032 (ttp-170) cc_final: 0.7817 (ttp-170) REVERT: C 107 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.5711 (mm-30) REVERT: C 109 MET cc_start: 0.7947 (mtp) cc_final: 0.7744 (mtm) REVERT: C 117 ASN cc_start: 0.8170 (m-40) cc_final: 0.7778 (m-40) REVERT: C 240 ASP cc_start: 0.7925 (m-30) cc_final: 0.7574 (m-30) REVERT: C 293 HIS cc_start: 0.7499 (m-70) cc_final: 0.6364 (t-90) REVERT: C 325 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7498 (tp30) REVERT: C 329 LYS cc_start: 0.7727 (mttt) cc_final: 0.7302 (mtpm) REVERT: C 352 ASP cc_start: 0.7841 (m-30) cc_final: 0.7458 (m-30) REVERT: C 353 LYS cc_start: 0.6773 (ttpp) cc_final: 0.6419 (tptp) REVERT: C 357 LEU cc_start: 0.7302 (mt) cc_final: 0.6843 (mt) REVERT: C 367 LYS cc_start: 0.8381 (tttt) cc_final: 0.8016 (tttm) REVERT: C 380 TYR cc_start: 0.7615 (m-80) cc_final: 0.7138 (m-80) REVERT: C 409 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7356 (mtt) REVERT: C 416 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: C 435 LYS cc_start: 0.7698 (mttm) cc_final: 0.7439 (mttm) REVERT: D 31 ASP cc_start: 0.7355 (m-30) cc_final: 0.7006 (p0) REVERT: D 53 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7760 (mm-30) REVERT: D 57 LYS cc_start: 0.7867 (tttm) cc_final: 0.7479 (tttp) REVERT: D 69 GLN cc_start: 0.7990 (tp-100) cc_final: 0.7786 (tm-30) REVERT: D 84 GLU cc_start: 0.7461 (tp30) cc_final: 0.6958 (mm-30) REVERT: D 98 ARG cc_start: 0.8057 (ttp-170) cc_final: 0.7846 (ttp-170) REVERT: D 107 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.5727 (mm-30) REVERT: D 109 MET cc_start: 0.7966 (mtp) cc_final: 0.7758 (mtm) REVERT: D 117 ASN cc_start: 0.8184 (m-40) cc_final: 0.7791 (m-40) REVERT: D 240 ASP cc_start: 0.7920 (m-30) cc_final: 0.7560 (m-30) REVERT: D 293 HIS cc_start: 0.7506 (m-70) cc_final: 0.6367 (t-90) REVERT: D 325 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7508 (tp30) REVERT: D 329 LYS cc_start: 0.7738 (mttt) cc_final: 0.7318 (mtpm) REVERT: D 352 ASP cc_start: 0.7863 (m-30) cc_final: 0.7480 (m-30) REVERT: D 353 LYS cc_start: 0.6777 (ttpp) cc_final: 0.6427 (tptp) REVERT: D 357 LEU cc_start: 0.7320 (mt) cc_final: 0.6866 (mt) REVERT: D 367 LYS cc_start: 0.8380 (tttt) cc_final: 0.8011 (tttm) REVERT: D 380 TYR cc_start: 0.7604 (m-80) cc_final: 0.7133 (m-80) REVERT: D 409 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7355 (mtt) REVERT: D 416 ASP cc_start: 0.7684 (OUTLIER) cc_final: 0.7182 (m-30) REVERT: D 435 LYS cc_start: 0.7692 (mttm) cc_final: 0.7430 (mttm) outliers start: 50 outliers final: 8 residues processed: 296 average time/residue: 1.4811 time to fit residues: 480.4042 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 252 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 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 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 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 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: 2.9990 chunk 141 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 0.0980 chunk 155 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 161 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.145935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118534 restraints weight = 15542.009| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.40 r_work: 0.3168 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3527 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= 0.119 Angle : 0.492 6.511 20984 Z= 0.264 Chirality : 0.043 0.139 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.722 20.093 2104 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.98 % Allowed : 20.47 % Favored : 76.55 % 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: 1.09 (0.19), residues: 1964 helix: 1.64 (0.18), residues: 800 sheet: 0.22 (0.25), residues: 420 loop : 0.14 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 453 HIS 0.003 0.001 HIS C 236 PHE 0.007 0.001 PHE B 310 TYR 0.015 0.002 TYR B 351 ARG 0.001 0.000 ARG B 156 Details of bonding type rmsd hydrogen bonds : bond 0.03316 ( 720) hydrogen bonds : angle 5.05354 ( 2100) covalent geometry : bond 0.00272 (15496) covalent geometry : angle 0.49219 (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 328 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 1.600 Fit side-chains REVERT: A 31 ASP cc_start: 0.7358 (m-30) cc_final: 0.6986 (p0) REVERT: A 53 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7637 (mm-30) REVERT: A 57 LYS cc_start: 0.7738 (tttm) cc_final: 0.7216 (ttmt) REVERT: A 69 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7733 (tm-30) REVERT: A 84 GLU cc_start: 0.7373 (tp30) cc_final: 0.6910 (mm-30) REVERT: A 98 ARG cc_start: 0.7990 (ttp-170) cc_final: 0.7552 (ttm170) REVERT: A 107 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6224 (tp30) REVERT: A 220 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8572 (m110) REVERT: A 240 ASP cc_start: 0.7918 (m-30) cc_final: 0.7522 (m-30) REVERT: A 293 HIS cc_start: 0.7399 (m-70) cc_final: 0.6260 (t-90) REVERT: A 325 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7527 (tp30) REVERT: A 329 LYS cc_start: 0.7676 (mttt) cc_final: 0.7214 (mtpm) REVERT: A 352 ASP cc_start: 0.7830 (m-30) cc_final: 0.7474 (m-30) REVERT: A 353 LYS cc_start: 0.6716 (ttpp) cc_final: 0.6363 (tptp) REVERT: A 357 LEU cc_start: 0.7281 (mt) cc_final: 0.6836 (mt) REVERT: A 367 LYS cc_start: 0.8299 (tttt) cc_final: 0.7931 (tttm) REVERT: A 380 TYR cc_start: 0.7496 (m-80) cc_final: 0.6936 (m-80) REVERT: A 409 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: A 412 LYS cc_start: 0.7673 (mtmt) cc_final: 0.7276 (mtpt) REVERT: A 416 ASP cc_start: 0.7618 (m-30) cc_final: 0.7139 (m-30) REVERT: A 435 LYS cc_start: 0.7350 (mttm) cc_final: 0.7115 (mttm) REVERT: B 31 ASP cc_start: 0.7365 (m-30) cc_final: 0.6993 (p0) REVERT: B 53 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7668 (mm-30) REVERT: B 57 LYS cc_start: 0.7730 (tttm) cc_final: 0.7206 (ttmt) REVERT: B 69 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7731 (tm-30) REVERT: B 84 GLU cc_start: 0.7357 (tp30) cc_final: 0.6876 (mm-30) REVERT: B 98 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7540 (ttm170) REVERT: B 107 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6269 (tp30) REVERT: B 220 ASN cc_start: 0.8825 (OUTLIER) cc_final: 0.8568 (m110) REVERT: B 240 ASP cc_start: 0.7925 (m-30) cc_final: 0.7531 (m-30) REVERT: B 293 HIS cc_start: 0.7375 (m-70) cc_final: 0.6232 (t-90) REVERT: B 325 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7558 (tp30) REVERT: B 329 LYS cc_start: 0.7663 (mttt) cc_final: 0.7192 (mtpm) REVERT: B 352 ASP cc_start: 0.7821 (m-30) cc_final: 0.7463 (m-30) REVERT: B 353 LYS cc_start: 0.6724 (ttpp) cc_final: 0.6360 (tptp) REVERT: B 357 LEU cc_start: 0.7283 (mt) cc_final: 0.6839 (mt) REVERT: B 367 LYS cc_start: 0.8301 (tttt) cc_final: 0.7935 (tttm) REVERT: B 380 TYR cc_start: 0.7488 (m-80) cc_final: 0.6925 (m-80) REVERT: B 409 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7178 (mtt) REVERT: B 412 LYS cc_start: 0.7633 (mtmt) cc_final: 0.7258 (mtpt) REVERT: B 416 ASP cc_start: 0.7637 (m-30) cc_final: 0.7179 (m-30) REVERT: B 435 LYS cc_start: 0.7348 (mttm) cc_final: 0.7116 (mttm) REVERT: C 31 ASP cc_start: 0.7358 (m-30) cc_final: 0.6993 (p0) REVERT: C 53 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7662 (mm-30) REVERT: C 57 LYS cc_start: 0.7715 (tttm) cc_final: 0.7198 (ttmt) REVERT: C 69 GLN cc_start: 0.7936 (tp-100) cc_final: 0.7732 (tm-30) REVERT: C 84 GLU cc_start: 0.7364 (tp30) cc_final: 0.6890 (mm-30) REVERT: C 98 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7532 (ttm170) REVERT: C 107 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.6229 (tp30) REVERT: C 220 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8569 (m110) REVERT: C 240 ASP cc_start: 0.7927 (m-30) cc_final: 0.7514 (m-30) REVERT: C 293 HIS cc_start: 0.7388 (m-70) cc_final: 0.6258 (t-90) REVERT: C 325 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7527 (tp30) REVERT: C 329 LYS cc_start: 0.7658 (mttt) cc_final: 0.7193 (mtpm) REVERT: C 352 ASP cc_start: 0.7794 (m-30) cc_final: 0.7434 (m-30) REVERT: C 353 LYS cc_start: 0.6711 (ttpp) cc_final: 0.6358 (tptp) REVERT: C 357 LEU cc_start: 0.7284 (mt) cc_final: 0.6837 (mt) REVERT: C 367 LYS cc_start: 0.8282 (tttt) cc_final: 0.7915 (tttm) REVERT: C 380 TYR cc_start: 0.7505 (m-80) cc_final: 0.7011 (m-80) REVERT: C 409 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7192 (mtt) REVERT: C 416 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7147 (m-30) REVERT: C 435 LYS cc_start: 0.7338 (mttm) cc_final: 0.7060 (mttm) REVERT: D 31 ASP cc_start: 0.7344 (m-30) cc_final: 0.6984 (p0) REVERT: D 53 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7656 (mm-30) REVERT: D 57 LYS cc_start: 0.7720 (tttm) cc_final: 0.7208 (ttmt) REVERT: D 69 GLN cc_start: 0.7939 (tp-100) cc_final: 0.7732 (tm-30) REVERT: D 84 GLU cc_start: 0.7355 (tp30) cc_final: 0.6894 (mm-30) REVERT: D 98 ARG cc_start: 0.7980 (ttp-170) cc_final: 0.7540 (ttm170) REVERT: D 107 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.6254 (tp30) REVERT: D 220 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8570 (m110) REVERT: D 240 ASP cc_start: 0.7898 (m-30) cc_final: 0.7503 (m-30) REVERT: D 293 HIS cc_start: 0.7363 (m-70) cc_final: 0.6218 (t-90) REVERT: D 325 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7507 (tp30) REVERT: D 329 LYS cc_start: 0.7667 (mttt) cc_final: 0.7207 (mtpm) REVERT: D 352 ASP cc_start: 0.7813 (m-30) cc_final: 0.7456 (m-30) REVERT: D 353 LYS cc_start: 0.6721 (ttpp) cc_final: 0.6368 (tptp) REVERT: D 357 LEU cc_start: 0.7299 (mt) cc_final: 0.6855 (mt) REVERT: D 367 LYS cc_start: 0.8300 (tttt) cc_final: 0.7933 (tttm) REVERT: D 380 TYR cc_start: 0.7484 (m-80) cc_final: 0.6990 (m-80) REVERT: D 409 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7206 (mtt) REVERT: D 416 ASP cc_start: 0.7623 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: D 435 LYS cc_start: 0.7333 (mttm) cc_final: 0.7056 (mttm) outliers start: 48 outliers final: 12 residues processed: 314 average time/residue: 1.2865 time to fit residues: 445.7236 Evaluate side-chains 286 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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 220 ASN 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 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 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 220 ASN Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 118 optimal weight: 0.0020 chunk 179 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 overall best weight: 1.3794 ------------------------------------------------------------------------------- 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 C 110 ASN C 117 ASN D 110 ASN D 117 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.144527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.118124 restraints weight = 15483.507| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.29 r_work: 0.3165 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15496 Z= 0.176 Angle : 0.540 7.261 20984 Z= 0.288 Chirality : 0.046 0.315 2324 Planarity : 0.004 0.031 2716 Dihedral : 4.787 20.666 2104 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.60 % Allowed : 19.98 % Favored : 76.43 % 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: 1.04 (0.19), residues: 1964 helix: 1.51 (0.18), residues: 804 sheet: 0.30 (0.26), residues: 408 loop : 0.16 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 178 HIS 0.003 0.001 HIS C 30 PHE 0.010 0.002 PHE D 38 TYR 0.020 0.002 TYR B 351 ARG 0.002 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 720) hydrogen bonds : angle 5.08230 ( 2100) covalent geometry : bond 0.00422 (15496) covalent geometry : angle 0.54025 (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 316 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 1.666 Fit side-chains REVERT: A 31 ASP cc_start: 0.7388 (m-30) cc_final: 0.7031 (p0) REVERT: A 53 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7566 (mm-30) REVERT: A 57 LYS cc_start: 0.7746 (tttm) cc_final: 0.7238 (ttmt) REVERT: A 84 GLU cc_start: 0.7381 (tp30) cc_final: 0.6892 (mm-30) REVERT: A 98 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7565 (ttm170) REVERT: A 107 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6313 (tp30) REVERT: A 240 ASP cc_start: 0.7892 (m-30) cc_final: 0.7532 (m-30) REVERT: A 293 HIS cc_start: 0.7428 (m-70) cc_final: 0.6291 (t-90) REVERT: A 313 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6747 (pm20) REVERT: A 325 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7526 (tp30) REVERT: A 329 LYS cc_start: 0.7597 (mttt) cc_final: 0.7144 (mtpm) REVERT: A 352 ASP cc_start: 0.7834 (m-30) cc_final: 0.7498 (m-30) REVERT: A 353 LYS cc_start: 0.6803 (ttpp) cc_final: 0.6412 (tptp) REVERT: A 357 LEU cc_start: 0.7319 (mt) cc_final: 0.6909 (mt) REVERT: A 367 LYS cc_start: 0.8315 (tttt) cc_final: 0.7952 (tttm) REVERT: A 380 TYR cc_start: 0.7515 (m-80) cc_final: 0.6997 (m-80) REVERT: A 409 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7187 (mtt) REVERT: A 412 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7443 (mtpt) REVERT: A 416 ASP cc_start: 0.7585 (OUTLIER) cc_final: 0.7158 (m-30) REVERT: A 435 LYS cc_start: 0.7465 (mttm) cc_final: 0.7263 (mttm) REVERT: B 31 ASP cc_start: 0.7400 (m-30) cc_final: 0.7036 (p0) REVERT: B 53 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 57 LYS cc_start: 0.7741 (tttm) cc_final: 0.7233 (ttmt) REVERT: B 84 GLU cc_start: 0.7353 (tp30) cc_final: 0.6887 (mm-30) REVERT: B 98 ARG cc_start: 0.7979 (ttp-170) cc_final: 0.7545 (ttm170) REVERT: B 107 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6338 (tp30) REVERT: B 240 ASP cc_start: 0.7890 (m-30) cc_final: 0.7534 (m-30) REVERT: B 293 HIS cc_start: 0.7404 (m-70) cc_final: 0.6283 (t-90) REVERT: B 313 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: B 325 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7546 (tp30) REVERT: B 329 LYS cc_start: 0.7590 (mttt) cc_final: 0.7132 (mtpm) REVERT: B 352 ASP cc_start: 0.7821 (m-30) cc_final: 0.7483 (m-30) REVERT: B 353 LYS cc_start: 0.6810 (ttpp) cc_final: 0.6411 (tptp) REVERT: B 357 LEU cc_start: 0.7325 (mt) cc_final: 0.6915 (mt) REVERT: B 367 LYS cc_start: 0.8326 (tttt) cc_final: 0.7969 (tttm) REVERT: B 380 TYR cc_start: 0.7511 (m-80) cc_final: 0.6988 (m-80) REVERT: B 409 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7187 (mtt) REVERT: B 412 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7442 (mtpt) REVERT: B 416 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7007 (m-30) REVERT: B 435 LYS cc_start: 0.7456 (mttm) cc_final: 0.7256 (mttm) REVERT: C 31 ASP cc_start: 0.7389 (m-30) cc_final: 0.7038 (p0) REVERT: C 53 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7572 (mm-30) REVERT: C 57 LYS cc_start: 0.7736 (tttm) cc_final: 0.7229 (ttmt) REVERT: C 69 GLN cc_start: 0.7913 (tp-100) cc_final: 0.7711 (tm-30) REVERT: C 84 GLU cc_start: 0.7371 (tp30) cc_final: 0.6868 (mm-30) REVERT: C 98 ARG cc_start: 0.7960 (ttp-170) cc_final: 0.7527 (ttm170) REVERT: C 107 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.6323 (tp30) REVERT: C 240 ASP cc_start: 0.7915 (m-30) cc_final: 0.7531 (m-30) REVERT: C 293 HIS cc_start: 0.7411 (m-70) cc_final: 0.6306 (t-90) REVERT: C 325 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7516 (tp30) REVERT: C 329 LYS cc_start: 0.7578 (mttt) cc_final: 0.7122 (mtpm) REVERT: C 352 ASP cc_start: 0.7822 (m-30) cc_final: 0.7484 (m-30) REVERT: C 353 LYS cc_start: 0.6808 (ttpp) cc_final: 0.6414 (tptp) REVERT: C 357 LEU cc_start: 0.7326 (mt) cc_final: 0.6916 (mt) REVERT: C 367 LYS cc_start: 0.8332 (tttt) cc_final: 0.7983 (tttm) REVERT: C 380 TYR cc_start: 0.7530 (m-80) cc_final: 0.7001 (m-80) REVERT: C 409 MET cc_start: 0.8250 (OUTLIER) cc_final: 0.7215 (mtt) REVERT: C 416 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7146 (m-30) REVERT: C 435 LYS cc_start: 0.7464 (mttm) cc_final: 0.7158 (mttm) REVERT: D 31 ASP cc_start: 0.7379 (m-30) cc_final: 0.7028 (p0) REVERT: D 53 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 57 LYS cc_start: 0.7709 (tttm) cc_final: 0.7222 (ttmt) REVERT: D 69 GLN cc_start: 0.7909 (tp-100) cc_final: 0.7709 (tm-30) REVERT: D 84 GLU cc_start: 0.7363 (tp30) cc_final: 0.6886 (mm-30) REVERT: D 98 ARG cc_start: 0.7983 (ttp-170) cc_final: 0.7556 (ttm170) REVERT: D 107 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6316 (tp30) REVERT: D 240 ASP cc_start: 0.7838 (m-30) cc_final: 0.7485 (m-30) REVERT: D 293 HIS cc_start: 0.7408 (m-70) cc_final: 0.6282 (t-90) REVERT: D 325 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7518 (tp30) REVERT: D 329 LYS cc_start: 0.7599 (mttt) cc_final: 0.7153 (mtpm) REVERT: D 352 ASP cc_start: 0.7831 (m-30) cc_final: 0.7491 (m-30) REVERT: D 353 LYS cc_start: 0.6791 (ttpp) cc_final: 0.6397 (tptp) REVERT: D 357 LEU cc_start: 0.7330 (mt) cc_final: 0.6920 (mt) REVERT: D 367 LYS cc_start: 0.8335 (tttt) cc_final: 0.7980 (tttm) REVERT: D 380 TYR cc_start: 0.7521 (m-80) cc_final: 0.6999 (m-80) REVERT: D 409 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.7220 (mtt) REVERT: D 416 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7165 (m-30) REVERT: D 435 LYS cc_start: 0.7460 (mttm) cc_final: 0.7150 (mttm) outliers start: 58 outliers final: 16 residues processed: 294 average time/residue: 1.2878 time to fit residues: 417.3928 Evaluate side-chains 272 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 242 time to evaluate : 2.206 ------------------------------------------------------------------------------- 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 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 97 GLU 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 97 GLU 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 70 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 185 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 22 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 121 ASN B 220 ASN C 19 GLN C 117 ASN C 220 ASN D 19 GLN D 117 ASN D 220 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.145375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118294 restraints weight = 15583.145| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.38 r_work: 0.3156 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15496 Z= 0.146 Angle : 0.520 6.925 20984 Z= 0.276 Chirality : 0.045 0.276 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.679 19.854 2104 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.16 % Allowed : 20.22 % Favored : 76.61 % 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: 1.62 (0.18), residues: 800 sheet: 0.23 (0.26), residues: 420 loop : 0.12 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 178 HIS 0.003 0.001 HIS C 30 PHE 0.011 0.002 PHE D 38 TYR 0.021 0.002 TYR B 351 ARG 0.002 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 720) hydrogen bonds : angle 5.01483 ( 2100) covalent geometry : bond 0.00350 (15496) covalent geometry : angle 0.52027 (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 320 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 269 time to evaluate : 2.826 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7506 (m-30) cc_final: 0.7088 (p0) REVERT: A 53 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 57 LYS cc_start: 0.7655 (tttm) cc_final: 0.7243 (ttmt) REVERT: A 84 GLU cc_start: 0.7408 (tp30) cc_final: 0.6902 (mm-30) REVERT: A 107 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6363 (tp30) REVERT: A 220 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (m-40) REVERT: A 240 ASP cc_start: 0.8037 (m-30) cc_final: 0.7663 (m-30) REVERT: A 293 HIS cc_start: 0.7391 (m-70) cc_final: 0.6255 (t-90) REVERT: A 313 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6723 (pm20) REVERT: A 325 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7547 (tp30) REVERT: A 329 LYS cc_start: 0.7549 (mttt) cc_final: 0.7083 (mtpm) REVERT: A 353 LYS cc_start: 0.6851 (ttpp) cc_final: 0.6436 (tptt) REVERT: A 357 LEU cc_start: 0.7341 (mt) cc_final: 0.6930 (mt) REVERT: A 367 LYS cc_start: 0.8291 (tttt) cc_final: 0.7934 (tttm) REVERT: A 380 TYR cc_start: 0.7396 (m-80) cc_final: 0.6949 (m-80) REVERT: A 409 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7204 (mtt) REVERT: A 412 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7434 (mtpt) REVERT: A 416 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7145 (m-30) REVERT: A 481 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6088 (m-80) REVERT: B 31 ASP cc_start: 0.7502 (m-30) cc_final: 0.7084 (p0) REVERT: B 53 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 57 LYS cc_start: 0.7641 (tttm) cc_final: 0.7225 (ttmt) REVERT: B 84 GLU cc_start: 0.7357 (tp30) cc_final: 0.6912 (mm-30) REVERT: B 107 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6385 (tp30) REVERT: B 220 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8704 (m-40) REVERT: B 240 ASP cc_start: 0.8029 (m-30) cc_final: 0.7656 (m-30) REVERT: B 253 LEU cc_start: 0.8228 (mt) cc_final: 0.7919 (mm) REVERT: B 293 HIS cc_start: 0.7377 (m-70) cc_final: 0.6239 (t-90) REVERT: B 313 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6733 (pm20) REVERT: B 325 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7608 (tp30) REVERT: B 329 LYS cc_start: 0.7540 (mttt) cc_final: 0.7070 (mtpm) REVERT: B 352 ASP cc_start: 0.7784 (m-30) cc_final: 0.7440 (m-30) REVERT: B 353 LYS cc_start: 0.6864 (ttpp) cc_final: 0.6444 (tptt) REVERT: B 357 LEU cc_start: 0.7352 (mt) cc_final: 0.6943 (mt) REVERT: B 367 LYS cc_start: 0.8298 (tttt) cc_final: 0.7946 (tttm) REVERT: B 380 TYR cc_start: 0.7377 (m-80) cc_final: 0.6928 (m-80) REVERT: B 409 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7202 (mtt) REVERT: B 481 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: C 31 ASP cc_start: 0.7489 (m-30) cc_final: 0.7080 (p0) REVERT: C 53 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7557 (mm-30) REVERT: C 57 LYS cc_start: 0.7637 (tttm) cc_final: 0.7225 (ttmt) REVERT: C 84 GLU cc_start: 0.7388 (tp30) cc_final: 0.6892 (mm-30) REVERT: C 107 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6383 (tp30) REVERT: C 220 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8683 (m-40) REVERT: C 240 ASP cc_start: 0.8023 (m-30) cc_final: 0.7627 (m-30) REVERT: C 293 HIS cc_start: 0.7369 (m-70) cc_final: 0.6251 (t-90) REVERT: C 325 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7586 (tp30) REVERT: C 329 LYS cc_start: 0.7530 (mttt) cc_final: 0.7060 (mtpm) REVERT: C 352 ASP cc_start: 0.7754 (m-30) cc_final: 0.7411 (m-30) REVERT: C 353 LYS cc_start: 0.6850 (ttpp) cc_final: 0.6433 (tptt) REVERT: C 357 LEU cc_start: 0.7345 (mt) cc_final: 0.6935 (mt) REVERT: C 367 LYS cc_start: 0.8306 (tttt) cc_final: 0.7963 (tttm) REVERT: C 380 TYR cc_start: 0.7395 (m-80) cc_final: 0.6938 (m-80) REVERT: C 409 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7202 (mtt) REVERT: C 416 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7180 (m-30) REVERT: C 435 LYS cc_start: 0.7337 (mttm) cc_final: 0.7101 (mttm) REVERT: C 481 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.6119 (m-80) REVERT: D 31 ASP cc_start: 0.7492 (m-30) cc_final: 0.7079 (p0) REVERT: D 53 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7555 (mm-30) REVERT: D 57 LYS cc_start: 0.7634 (tttm) cc_final: 0.7222 (ttmt) REVERT: D 84 GLU cc_start: 0.7369 (tp30) cc_final: 0.6922 (mm-30) REVERT: D 107 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: D 220 ASN cc_start: 0.8918 (OUTLIER) cc_final: 0.8690 (m-40) REVERT: D 240 ASP cc_start: 0.7947 (m-30) cc_final: 0.7536 (m-30) REVERT: D 293 HIS cc_start: 0.7369 (m-70) cc_final: 0.6228 (t-90) REVERT: D 325 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7582 (tp30) REVERT: D 329 LYS cc_start: 0.7550 (mttt) cc_final: 0.7088 (mtpm) REVERT: D 352 ASP cc_start: 0.7778 (m-30) cc_final: 0.7434 (m-30) REVERT: D 353 LYS cc_start: 0.6842 (ttpp) cc_final: 0.6430 (tptt) REVERT: D 357 LEU cc_start: 0.7363 (mt) cc_final: 0.6954 (mt) REVERT: D 367 LYS cc_start: 0.8308 (tttt) cc_final: 0.7959 (tttm) REVERT: D 380 TYR cc_start: 0.7377 (m-80) cc_final: 0.6923 (m-80) REVERT: D 409 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7243 (mtt) REVERT: D 416 ASP cc_start: 0.7626 (m-30) cc_final: 0.7180 (m-30) REVERT: D 435 LYS cc_start: 0.7368 (mttm) cc_final: 0.7124 (mttm) REVERT: D 481 TYR cc_start: 0.7011 (OUTLIER) cc_final: 0.6094 (m-80) outliers start: 51 outliers final: 17 residues processed: 297 average time/residue: 1.8233 time to fit residues: 597.5985 Evaluate side-chains 288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 253 time to evaluate : 1.665 ------------------------------------------------------------------------------- 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 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 220 ASN 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 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 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 220 ASN Chi-restraints excluded: chain D residue 409 MET 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: 4.9990 chunk 67 optimal weight: 0.9990 chunk 20 optimal weight: 0.0770 chunk 167 optimal weight: 0.0770 chunk 178 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.0050 chunk 150 optimal weight: 0.0770 chunk 98 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.1868 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 220 ASN B 19 GLN B 220 ASN C 19 GLN C 220 ASN D 19 GLN D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.148163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121863 restraints weight = 15479.287| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.28 r_work: 0.3204 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15496 Z= 0.094 Angle : 0.477 6.865 20984 Z= 0.253 Chirality : 0.043 0.241 2324 Planarity : 0.004 0.032 2716 Dihedral : 4.409 17.825 2104 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.92 % Allowed : 21.96 % Favored : 75.12 % 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: 1.26 (0.19), residues: 1964 helix: 1.80 (0.18), residues: 800 sheet: 0.21 (0.27), residues: 380 loop : 0.27 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 453 HIS 0.001 0.000 HIS D 236 PHE 0.009 0.001 PHE C 38 TYR 0.016 0.001 TYR B 351 ARG 0.001 0.000 ARG C 321 Details of bonding type rmsd hydrogen bonds : bond 0.02969 ( 720) hydrogen bonds : angle 4.83061 ( 2100) covalent geometry : bond 0.00210 (15496) covalent geometry : angle 0.47684 (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: 47 poor density : 259 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7493 (m-30) cc_final: 0.7056 (p0) REVERT: A 53 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7550 (mm-30) REVERT: A 57 LYS cc_start: 0.7620 (tttm) cc_final: 0.7196 (ttmt) REVERT: A 84 GLU cc_start: 0.7357 (tp30) cc_final: 0.6909 (mm-30) REVERT: A 90 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: A 107 GLU cc_start: 0.6718 (OUTLIER) cc_final: 0.6271 (tp30) REVERT: A 109 MET cc_start: 0.7781 (mtm) cc_final: 0.7579 (mtm) REVERT: A 220 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8471 (m110) REVERT: A 240 ASP cc_start: 0.7916 (m-30) cc_final: 0.7551 (m-30) REVERT: A 253 LEU cc_start: 0.8279 (mt) cc_final: 0.7991 (mm) REVERT: A 313 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6700 (pm20) REVERT: A 325 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7558 (tp30) REVERT: A 329 LYS cc_start: 0.7495 (mttt) cc_final: 0.7060 (mtpm) REVERT: A 353 LYS cc_start: 0.6766 (ttpp) cc_final: 0.6405 (tptt) REVERT: A 357 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6917 (mt) REVERT: A 367 LYS cc_start: 0.8321 (tttt) cc_final: 0.8002 (tttm) REVERT: A 380 TYR cc_start: 0.7359 (m-80) cc_final: 0.6840 (m-80) REVERT: A 481 TYR cc_start: 0.6910 (OUTLIER) cc_final: 0.6042 (m-80) REVERT: B 31 ASP cc_start: 0.7543 (m-30) cc_final: 0.7111 (p0) REVERT: B 53 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7565 (mm-30) REVERT: B 57 LYS cc_start: 0.7610 (tttm) cc_final: 0.7181 (ttmt) REVERT: B 84 GLU cc_start: 0.7343 (tp30) cc_final: 0.6935 (mm-30) REVERT: B 107 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6305 (tp30) REVERT: B 109 MET cc_start: 0.7791 (mtm) cc_final: 0.7588 (mtm) REVERT: B 138 ASP cc_start: 0.8325 (p0) cc_final: 0.7992 (p0) REVERT: B 220 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8475 (m110) REVERT: B 240 ASP cc_start: 0.7912 (m-30) cc_final: 0.7555 (m-30) REVERT: B 253 LEU cc_start: 0.8281 (mt) cc_final: 0.7996 (mm) REVERT: B 293 HIS cc_start: 0.7329 (m-70) cc_final: 0.6267 (t-90) REVERT: B 325 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7557 (tp30) REVERT: B 329 LYS cc_start: 0.7485 (mttt) cc_final: 0.7025 (mtpm) REVERT: B 352 ASP cc_start: 0.7765 (m-30) cc_final: 0.7437 (m-30) REVERT: B 353 LYS cc_start: 0.6767 (ttpp) cc_final: 0.6396 (tptt) REVERT: B 357 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6911 (mt) REVERT: B 367 LYS cc_start: 0.8318 (tttt) cc_final: 0.8001 (tttm) REVERT: B 380 TYR cc_start: 0.7344 (m-80) cc_final: 0.6817 (m-80) REVERT: B 481 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6053 (m-80) REVERT: C 31 ASP cc_start: 0.7527 (m-30) cc_final: 0.7116 (p0) REVERT: C 53 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7554 (mm-30) REVERT: C 57 LYS cc_start: 0.7609 (tttm) cc_final: 0.7182 (ttmt) REVERT: C 84 GLU cc_start: 0.7342 (tp30) cc_final: 0.6890 (mm-30) REVERT: C 90 TYR cc_start: 0.7531 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: C 107 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6306 (tp30) REVERT: C 109 MET cc_start: 0.7803 (mtm) cc_final: 0.7602 (mtm) REVERT: C 220 ASN cc_start: 0.8727 (OUTLIER) cc_final: 0.8470 (m110) REVERT: C 240 ASP cc_start: 0.7918 (m-30) cc_final: 0.7561 (m-30) REVERT: C 325 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7549 (tp30) REVERT: C 329 LYS cc_start: 0.7464 (mttt) cc_final: 0.7018 (mtpm) REVERT: C 353 LYS cc_start: 0.6773 (ttpp) cc_final: 0.6406 (tptt) REVERT: C 357 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.6913 (mt) REVERT: C 367 LYS cc_start: 0.8321 (tttt) cc_final: 0.8007 (tttm) REVERT: C 380 TYR cc_start: 0.7346 (m-80) cc_final: 0.6866 (m-80) REVERT: C 481 TYR cc_start: 0.6941 (OUTLIER) cc_final: 0.6081 (m-80) REVERT: D 31 ASP cc_start: 0.7488 (m-30) cc_final: 0.7058 (p0) REVERT: D 53 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7551 (mm-30) REVERT: D 57 LYS cc_start: 0.7606 (tttm) cc_final: 0.7178 (ttmt) REVERT: D 84 GLU cc_start: 0.7365 (tp30) cc_final: 0.6932 (mm-30) REVERT: D 107 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6283 (tp30) REVERT: D 109 MET cc_start: 0.7811 (mtm) cc_final: 0.7609 (mtm) REVERT: D 138 ASP cc_start: 0.8313 (p0) cc_final: 0.7983 (p0) REVERT: D 220 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8476 (m110) REVERT: D 240 ASP cc_start: 0.7907 (m-30) cc_final: 0.7551 (m-30) REVERT: D 293 HIS cc_start: 0.7317 (m-70) cc_final: 0.6253 (t-90) REVERT: D 325 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7534 (tp30) REVERT: D 329 LYS cc_start: 0.7485 (mttt) cc_final: 0.7036 (mtpm) REVERT: D 353 LYS cc_start: 0.6763 (ttpp) cc_final: 0.6407 (tptt) REVERT: D 357 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6924 (mt) REVERT: D 367 LYS cc_start: 0.8319 (tttt) cc_final: 0.7998 (tttm) REVERT: D 380 TYR cc_start: 0.7341 (m-80) cc_final: 0.6862 (m-80) REVERT: D 481 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.6037 (m-80) outliers start: 47 outliers final: 8 residues processed: 280 average time/residue: 1.3148 time to fit residues: 406.3049 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 247 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 481 TYR Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 481 TYR Chi-restraints excluded: chain C residue 90 TYR Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain C residue 481 TYR Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 107 GLU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 416 ASP 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: 4.9990 chunk 183 optimal weight: 3.9990 chunk 167 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 13 optimal weight: 0.0770 chunk 175 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 153 optimal weight: 0.4980 overall best weight: 1.1340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.146218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.119299 restraints weight = 15537.839| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.36 r_work: 0.3173 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15496 Z= 0.153 Angle : 0.518 7.423 20984 Z= 0.275 Chirality : 0.045 0.244 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.481 18.536 2104 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.23 % Allowed : 22.08 % Favored : 74.69 % 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: 1.19 (0.19), residues: 1964 helix: 1.71 (0.18), residues: 804 sheet: 0.19 (0.27), residues: 404 loop : 0.28 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 178 HIS 0.002 0.001 HIS A 30 PHE 0.009 0.002 PHE D 38 TYR 0.019 0.002 TYR C 351 ARG 0.003 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 720) hydrogen bonds : angle 4.87171 ( 2100) covalent geometry : bond 0.00373 (15496) covalent geometry : angle 0.51800 (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 305 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 253 time to evaluate : 1.684 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7445 (m-30) cc_final: 0.7026 (p0) REVERT: A 53 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7571 (mm-30) REVERT: A 57 LYS cc_start: 0.7671 (tttm) cc_final: 0.7263 (ttmt) REVERT: A 84 GLU cc_start: 0.7342 (tp30) cc_final: 0.6874 (mm-30) REVERT: A 107 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: A 127 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8383 (mp) REVERT: A 220 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8588 (m110) REVERT: A 240 ASP cc_start: 0.7963 (m-30) cc_final: 0.7581 (m-30) REVERT: A 253 LEU cc_start: 0.8256 (mt) cc_final: 0.7955 (mm) REVERT: A 293 HIS cc_start: 0.7337 (m-70) cc_final: 0.6225 (t-90) REVERT: A 313 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6721 (pm20) REVERT: A 325 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7552 (tp30) REVERT: A 329 LYS cc_start: 0.7465 (mttt) cc_final: 0.7012 (mtpm) REVERT: A 353 LYS cc_start: 0.6819 (ttpp) cc_final: 0.6388 (tptt) REVERT: A 357 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6874 (mt) REVERT: A 367 LYS cc_start: 0.8302 (tttt) cc_final: 0.7973 (tttm) REVERT: A 380 TYR cc_start: 0.7348 (m-80) cc_final: 0.6855 (m-80) REVERT: A 409 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7083 (mtm) REVERT: A 416 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: A 481 TYR cc_start: 0.7039 (OUTLIER) cc_final: 0.6089 (m-80) REVERT: B 31 ASP cc_start: 0.7442 (m-30) cc_final: 0.7019 (p0) REVERT: B 53 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7569 (mm-30) REVERT: B 57 LYS cc_start: 0.7655 (tttm) cc_final: 0.7245 (ttmt) REVERT: B 84 GLU cc_start: 0.7337 (tp30) cc_final: 0.6876 (mm-30) REVERT: B 107 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6341 (tp30) REVERT: B 127 ILE cc_start: 0.8675 (OUTLIER) cc_final: 0.8378 (mp) REVERT: B 220 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8592 (m110) REVERT: B 240 ASP cc_start: 0.7964 (m-30) cc_final: 0.7586 (m-30) REVERT: B 253 LEU cc_start: 0.8264 (mt) cc_final: 0.7963 (mm) REVERT: B 293 HIS cc_start: 0.7329 (m-70) cc_final: 0.6237 (t-90) REVERT: B 325 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7525 (tp30) REVERT: B 329 LYS cc_start: 0.7470 (mttt) cc_final: 0.7084 (mtpm) REVERT: B 352 ASP cc_start: 0.7773 (m-30) cc_final: 0.7436 (m-30) REVERT: B 353 LYS cc_start: 0.6826 (ttpp) cc_final: 0.6393 (tptt) REVERT: B 357 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6876 (mt) REVERT: B 367 LYS cc_start: 0.8313 (tttt) cc_final: 0.7990 (tttm) REVERT: B 380 TYR cc_start: 0.7331 (m-80) cc_final: 0.6839 (m-80) REVERT: B 409 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7047 (mtm) REVERT: B 416 ASP cc_start: 0.7648 (OUTLIER) cc_final: 0.6947 (m-30) REVERT: B 481 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.6111 (m-80) REVERT: C 31 ASP cc_start: 0.7444 (m-30) cc_final: 0.7022 (p0) REVERT: C 53 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7553 (mm-30) REVERT: C 57 LYS cc_start: 0.7659 (tttm) cc_final: 0.7248 (ttmt) REVERT: C 84 GLU cc_start: 0.7346 (tp30) cc_final: 0.6864 (mm-30) REVERT: C 107 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.6310 (tp30) REVERT: C 127 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8386 (mp) REVERT: C 220 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8547 (m110) REVERT: C 240 ASP cc_start: 0.7960 (m-30) cc_final: 0.7583 (m-30) REVERT: C 293 HIS cc_start: 0.7332 (m-70) cc_final: 0.6238 (t-90) REVERT: C 325 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7463 (tp30) REVERT: C 329 LYS cc_start: 0.7510 (mttt) cc_final: 0.7121 (mtpm) REVERT: C 352 ASP cc_start: 0.7784 (m-30) cc_final: 0.7447 (m-30) REVERT: C 353 LYS cc_start: 0.6821 (ttpp) cc_final: 0.6385 (tptt) REVERT: C 357 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6876 (mt) REVERT: C 367 LYS cc_start: 0.8300 (tttt) cc_final: 0.7974 (tttm) REVERT: C 380 TYR cc_start: 0.7356 (m-80) cc_final: 0.6852 (m-80) REVERT: C 409 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7093 (mtm) REVERT: C 416 ASP cc_start: 0.7629 (OUTLIER) cc_final: 0.7154 (m-30) REVERT: C 481 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6101 (m-80) REVERT: D 31 ASP cc_start: 0.7431 (m-30) cc_final: 0.7013 (p0) REVERT: D 53 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7544 (mm-30) REVERT: D 57 LYS cc_start: 0.7641 (tttm) cc_final: 0.7236 (ttmt) REVERT: D 84 GLU cc_start: 0.7349 (tp30) cc_final: 0.6880 (mm-30) REVERT: D 107 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6317 (tp30) REVERT: D 127 ILE cc_start: 0.8666 (OUTLIER) cc_final: 0.8367 (mp) REVERT: D 220 ASN cc_start: 0.8820 (OUTLIER) cc_final: 0.8558 (m110) REVERT: D 240 ASP cc_start: 0.7960 (m-30) cc_final: 0.7577 (m-30) REVERT: D 293 HIS cc_start: 0.7333 (m-70) cc_final: 0.6229 (t-90) REVERT: D 325 GLU cc_start: 0.7847 (mm-30) cc_final: 0.7526 (tp30) REVERT: D 329 LYS cc_start: 0.7522 (mttt) cc_final: 0.7138 (mtpm) REVERT: D 352 ASP cc_start: 0.7784 (m-30) cc_final: 0.7448 (m-30) REVERT: D 353 LYS cc_start: 0.6822 (ttpp) cc_final: 0.6392 (tptt) REVERT: D 357 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.6879 (mt) REVERT: D 367 LYS cc_start: 0.8307 (tttt) cc_final: 0.7979 (tttm) REVERT: D 380 TYR cc_start: 0.7346 (m-80) cc_final: 0.6838 (m-80) REVERT: D 409 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.7112 (mtm) REVERT: D 481 TYR cc_start: 0.7034 (OUTLIER) cc_final: 0.6108 (m-80) outliers start: 52 outliers final: 13 residues processed: 284 average time/residue: 1.3533 time to fit residues: 424.7171 Evaluate side-chains 284 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.576 ------------------------------------------------------------------------------- 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 127 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 357 LEU 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 127 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 357 LEU 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 127 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 357 LEU 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 127 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 357 LEU 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: 1.9990 chunk 158 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 187 optimal weight: 4.9990 chunk 38 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.145555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.119053 restraints weight = 15744.706| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.28 r_work: 0.3168 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15496 Z= 0.160 Angle : 0.530 7.543 20984 Z= 0.280 Chirality : 0.045 0.242 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.530 18.716 2104 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.04 % Allowed : 22.08 % Favored : 74.88 % 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: 1.15 (0.19), residues: 1964 helix: 1.67 (0.18), residues: 804 sheet: 0.18 (0.27), residues: 404 loop : 0.26 (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 0.010 0.002 PHE C 38 TYR 0.019 0.002 TYR D 351 ARG 0.002 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03495 ( 720) hydrogen bonds : angle 4.90478 ( 2100) covalent geometry : bond 0.00388 (15496) covalent geometry : angle 0.52995 (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: 49 poor density : 243 time to evaluate : 1.791 Fit side-chains revert: symmetry clash REVERT: A 31 ASP cc_start: 0.7431 (m-30) cc_final: 0.7036 (p0) REVERT: A 53 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 57 LYS cc_start: 0.7749 (tttm) cc_final: 0.7340 (ttmt) REVERT: A 84 GLU cc_start: 0.7374 (tp30) cc_final: 0.6919 (mm-30) REVERT: A 107 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6365 (tp30) REVERT: A 220 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8574 (m110) REVERT: A 240 ASP cc_start: 0.7990 (m-30) cc_final: 0.7606 (m-30) REVERT: A 253 LEU cc_start: 0.8272 (mt) cc_final: 0.7961 (mm) REVERT: A 293 HIS cc_start: 0.7374 (m-70) cc_final: 0.6266 (t-90) REVERT: A 325 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7552 (tp30) REVERT: A 329 LYS cc_start: 0.7529 (mttt) cc_final: 0.7155 (mtpm) REVERT: A 353 LYS cc_start: 0.6826 (ttpp) cc_final: 0.6418 (tptt) REVERT: A 357 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.6923 (mt) REVERT: A 367 LYS cc_start: 0.8337 (tttt) cc_final: 0.8015 (tttm) REVERT: A 380 TYR cc_start: 0.7320 (m-80) cc_final: 0.6869 (m-80) REVERT: A 409 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7107 (mtm) REVERT: A 416 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: A 481 TYR cc_start: 0.6986 (OUTLIER) cc_final: 0.6079 (m-80) REVERT: B 31 ASP cc_start: 0.7429 (m-30) cc_final: 0.7031 (p0) REVERT: B 53 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 57 LYS cc_start: 0.7737 (tttm) cc_final: 0.7325 (ttmt) REVERT: B 84 GLU cc_start: 0.7377 (tp30) cc_final: 0.6923 (mm-30) REVERT: B 107 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6386 (tp30) REVERT: B 240 ASP cc_start: 0.7994 (m-30) cc_final: 0.7614 (m-30) REVERT: B 253 LEU cc_start: 0.8274 (mt) cc_final: 0.7961 (mm) REVERT: B 293 HIS cc_start: 0.7372 (m-70) cc_final: 0.6270 (t-90) REVERT: B 325 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7542 (tp30) REVERT: B 329 LYS cc_start: 0.7509 (mttt) cc_final: 0.7108 (mtpm) REVERT: B 353 LYS cc_start: 0.6826 (ttpp) cc_final: 0.6425 (tptt) REVERT: B 357 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6934 (mt) REVERT: B 367 LYS cc_start: 0.8352 (tttt) cc_final: 0.8037 (tttm) REVERT: B 380 TYR cc_start: 0.7298 (m-80) cc_final: 0.6849 (m-80) REVERT: B 409 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7072 (mtm) REVERT: B 416 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: B 481 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: C 31 ASP cc_start: 0.7422 (m-30) cc_final: 0.7034 (p0) REVERT: C 53 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7594 (mm-30) REVERT: C 57 LYS cc_start: 0.7736 (tttm) cc_final: 0.7328 (ttmt) REVERT: C 84 GLU cc_start: 0.7359 (tp30) cc_final: 0.6916 (mm-30) REVERT: C 107 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6364 (tp30) REVERT: C 220 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8572 (m110) REVERT: C 240 ASP cc_start: 0.7953 (m-30) cc_final: 0.7587 (m-30) REVERT: C 293 HIS cc_start: 0.7361 (m-70) cc_final: 0.6272 (t-90) REVERT: C 325 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7520 (tp30) REVERT: C 329 LYS cc_start: 0.7515 (mttt) cc_final: 0.7135 (mtpm) REVERT: C 352 ASP cc_start: 0.7812 (m-30) cc_final: 0.7477 (m-30) REVERT: C 353 LYS cc_start: 0.6847 (ttpp) cc_final: 0.6435 (tptt) REVERT: C 357 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6936 (mt) REVERT: C 367 LYS cc_start: 0.8336 (tttt) cc_final: 0.8016 (tttm) REVERT: C 380 TYR cc_start: 0.7322 (m-80) cc_final: 0.6866 (m-80) REVERT: C 409 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7132 (mtm) REVERT: C 416 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7186 (m-30) REVERT: C 481 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.6099 (m-80) REVERT: D 31 ASP cc_start: 0.7413 (m-30) cc_final: 0.7025 (p0) REVERT: D 53 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7573 (mm-30) REVERT: D 57 LYS cc_start: 0.7726 (tttm) cc_final: 0.7322 (ttmt) REVERT: D 84 GLU cc_start: 0.7383 (tp30) cc_final: 0.6928 (mm-30) REVERT: D 107 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6380 (tp30) REVERT: D 220 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8578 (m110) REVERT: D 240 ASP cc_start: 0.7976 (m-30) cc_final: 0.7586 (m-30) REVERT: D 293 HIS cc_start: 0.7368 (m-70) cc_final: 0.6259 (t-90) REVERT: D 325 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7545 (tp30) REVERT: D 329 LYS cc_start: 0.7528 (mttt) cc_final: 0.7160 (mtpm) REVERT: D 353 LYS cc_start: 0.6827 (ttpp) cc_final: 0.6421 (tptt) REVERT: D 357 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.6928 (mt) REVERT: D 367 LYS cc_start: 0.8337 (tttt) cc_final: 0.8016 (tttm) REVERT: D 380 TYR cc_start: 0.7307 (m-80) cc_final: 0.6846 (m-80) REVERT: D 409 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7126 (mtm) REVERT: D 481 TYR cc_start: 0.6989 (OUTLIER) cc_final: 0.6093 (m-80) outliers start: 49 outliers final: 13 residues processed: 272 average time/residue: 1.4169 time to fit residues: 423.7841 Evaluate side-chains 278 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 243 time to evaluate : 1.601 ------------------------------------------------------------------------------- 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 220 ASN Chi-restraints excluded: chain A residue 357 LEU 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 357 LEU 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 220 ASN Chi-restraints excluded: chain C residue 357 LEU 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 220 ASN Chi-restraints excluded: chain D residue 357 LEU 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: 0.8980 chunk 135 optimal weight: 0.8980 chunk 105 optimal weight: 0.0980 chunk 80 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 137 optimal weight: 0.5980 chunk 174 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 157 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 ASN B 19 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 ASN C 19 GLN ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 ASN D 19 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 220 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.147062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118872 restraints weight = 15679.297| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.39 r_work: 0.3187 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15496 Z= 0.114 Angle : 0.499 7.195 20984 Z= 0.265 Chirality : 0.044 0.228 2324 Planarity : 0.004 0.033 2716 Dihedral : 4.409 18.144 2104 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.17 % Allowed : 22.95 % Favored : 74.88 % 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: 1.23 (0.19), residues: 1964 helix: 1.71 (0.18), residues: 804 sheet: 0.20 (0.27), residues: 400 loop : 0.34 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.002 0.001 HIS B 30 PHE 0.009 0.001 PHE D 38 TYR 0.016 0.002 TYR D 351 ARG 0.003 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 720) hydrogen bonds : angle 4.87632 ( 2100) covalent geometry : bond 0.00271 (15496) covalent geometry : angle 0.49894 (20984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12370.80 seconds wall clock time: 216 minutes 47.03 seconds (13007.03 seconds total)