Starting phenix.real_space_refine on Thu Aug 6 17:48:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byl_45037/08_2026/9byl_45037_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byl_45037/08_2026/9byl_45037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2026/9byl_45037_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2026/9byl_45037_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2026/9byl_45037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2026/9byl_45037.map" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 10659 2.51 5 N 2718 2.21 5 O 3220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16706 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.38, per 1000 atoms: 0.20 Number of scatterers: 16706 At special positions: 0 Unit cell: (98.649, 131.193, 142.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 87 16.00 P 16 15.00 Mg 2 11.99 O 3220 8.00 N 2718 7.00 C 10659 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 743.6 milliseconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 12 sheets defined 63.0% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.095A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.987A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.962A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.674A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.065A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.580A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.665A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.398A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.622A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.116A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.052A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.961A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.678A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.897A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.648A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.713A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.007A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.072A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.529A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.365A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.484A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.488A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.179A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.066A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 Processing sheet with id=AB3, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.468A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2676 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.70 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4904 1.34 - 1.46: 3199 1.46 - 1.58: 8774 1.58 - 1.70: 25 1.70 - 1.82: 164 Bond restraints: 17066 Sorted by residual: bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 17061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 22264 2.10 - 4.19: 699 4.19 - 6.29: 74 6.29 - 8.38: 10 8.38 - 10.48: 9 Bond angle restraints: 23056 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.65 -6.11 1.36e+00 5.41e-01 2.02e+01 angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.36 5.84 1.30e+00 5.92e-01 2.02e+01 angle pdb=" OE1 GLN E 44 " pdb=" CD GLN E 44 " pdb=" NE2 GLN E 44 " ideal model delta sigma weight residual 122.60 118.53 4.07 1.00e+00 1.00e+00 1.65e+01 angle pdb=" C ALA E 26 " pdb=" N PRO E 27 " pdb=" CA PRO E 27 " ideal model delta sigma weight residual 119.19 123.50 -4.31 1.06e+00 8.90e-01 1.65e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.15 -4.44 1.15e+00 7.56e-01 1.49e+01 ... (remaining 23051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9501 25.06 - 50.12: 661 50.12 - 75.18: 129 75.18 - 100.25: 25 100.25 - 125.31: 2 Dihedral angle restraints: 10318 sinusoidal: 4314 harmonic: 6004 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.29 125.31 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.91 122.93 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.37 12.37 0 2.50e+00 1.60e-01 2.45e+01 ... (remaining 10315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2225 0.094 - 0.188: 208 0.188 - 0.281: 30 0.281 - 0.375: 3 0.375 - 0.469: 2 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2465 not shown) Planarity restraints: 2935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.077 2.00e-02 2.50e+03 3.69e-02 3.40e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 24 " 0.031 2.00e-02 2.50e+03 1.98e-02 6.83e+00 pdb=" CG PHE B 24 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 24 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 24 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 24 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 24 " 0.022 2.00e-02 2.50e+03 ... (remaining 2932 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 127 2.51 - 3.11: 11970 3.11 - 3.70: 28043 3.70 - 4.30: 42932 4.30 - 4.90: 67844 Nonbonded interactions: 150916 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 14.690 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.008 0.629 17067 Z= 0.429 Angle : 0.849 13.539 23058 Z= 0.512 Chirality : 0.059 0.469 2468 Planarity : 0.004 0.041 2935 Dihedral : 17.426 125.308 6459 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.45 % Allowed : 14.52 % Favored : 84.03 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.17), residues: 2016 helix: 0.60 (0.14), residues: 1185 sheet: 0.56 (0.38), residues: 149 loop : 0.24 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.029 0.002 TYR E 67 PHE 0.031 0.003 PHE B 24 TRP 0.077 0.005 TRP E 25 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00635 / 0.36 (17066) covalent geometry : angle 0.84408 / 0.51 (23056) SS BOND : bond 0.62925 / 33.12 ( 1) SS BOND : angle 9.71235 / 5.13 ( 2) hydrogen bonds : bond 0.15639 / 9.65 ( 908) hydrogen bonds : angle 6.57691 / 4.73 ( 2676) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 474 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8088 (p0) REVERT: A 246 SER cc_start: 0.8197 (m) cc_final: 0.7976 (p) REVERT: A 447 ASN cc_start: 0.8023 (m-40) cc_final: 0.7641 (m-40) REVERT: C 319 ASP cc_start: 0.7336 (m-30) cc_final: 0.6677 (m-30) outliers start: 26 outliers final: 8 residues processed: 492 average time/residue: 0.6367 time to fit residues: 348.4877 Evaluate side-chains 325 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 316 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 361 GLN A 410 ASN A 668 ASN B 150 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 84 HIS C 119 ASN C 238 ASN D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.098215 restraints weight = 22622.395| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.85 r_work: 0.2762 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17067 Z= 0.202 Angle : 0.610 12.253 23058 Z= 0.320 Chirality : 0.043 0.208 2468 Planarity : 0.004 0.042 2935 Dihedral : 9.431 127.075 2393 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.85 % Allowed : 17.53 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.18), residues: 2016 helix: 1.57 (0.15), residues: 1165 sheet: 0.38 (0.40), residues: 157 loop : 0.60 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.020 0.001 TYR D 105 PHE 0.016 0.001 PHE B 100 TRP 0.009 0.001 TRP B 9 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.20 (17066) covalent geometry : angle 0.60956 / 0.32 (23056) SS BOND : bond 0.00899 / 0.47 ( 1) SS BOND : angle 2.02843 / 1.08 ( 2) hydrogen bonds : bond 0.04641 / 2.91 ( 908) hydrogen bonds : angle 4.96527 / 3.57 ( 2676) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 308 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.9235 (m-30) cc_final: 0.8974 (m-30) REVERT: A 66 GLU cc_start: 0.8716 (tp30) cc_final: 0.8396 (tp30) REVERT: A 67 GLU cc_start: 0.8959 (mp0) cc_final: 0.8663 (mp0) REVERT: A 99 LYS cc_start: 0.8961 (mmtt) cc_final: 0.8752 (mmtp) REVERT: A 103 ASP cc_start: 0.9219 (m-30) cc_final: 0.8861 (m-30) REVERT: A 110 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.8562 (p0) REVERT: A 184 ARG cc_start: 0.8876 (ttm-80) cc_final: 0.8668 (ttm-80) REVERT: A 246 SER cc_start: 0.8093 (m) cc_final: 0.7703 (p) REVERT: A 270 ASP cc_start: 0.8539 (OUTLIER) cc_final: 0.7920 (OUTLIER) REVERT: A 274 ARG cc_start: 0.8368 (ptp-110) cc_final: 0.7914 (ptp-110) REVERT: A 286 ASP cc_start: 0.8964 (m-30) cc_final: 0.8382 (m-30) REVERT: A 362 ASP cc_start: 0.8685 (m-30) cc_final: 0.8284 (m-30) REVERT: A 384 GLU cc_start: 0.9401 (OUTLIER) cc_final: 0.8631 (pp20) REVERT: A 421 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 439 VAL cc_start: 0.9353 (t) cc_final: 0.9071 (p) REVERT: A 459 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8977 (mttm) REVERT: A 561 LEU cc_start: 0.9409 (tp) cc_final: 0.9166 (tp) REVERT: A 686 ARG cc_start: 0.8264 (mtp85) cc_final: 0.7951 (mtp85) REVERT: B 104 TYR cc_start: 0.9151 (m-80) cc_final: 0.8842 (m-80) REVERT: B 112 LYS cc_start: 0.9298 (mtmm) cc_final: 0.9066 (mtmm) REVERT: B 139 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8950 (mt-10) REVERT: B 274 ARG cc_start: 0.8213 (ttm-80) cc_final: 0.7898 (ttm110) REVERT: B 317 MET cc_start: 0.9129 (ptt) cc_final: 0.8904 (ptp) REVERT: B 321 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8548 (tm-30) REVERT: B 420 MET cc_start: 0.9549 (mmm) cc_final: 0.9309 (mmm) REVERT: B 483 GLU cc_start: 0.9068 (mp0) cc_final: 0.8624 (mp0) REVERT: B 603 GLU cc_start: 0.9107 (tt0) cc_final: 0.8498 (mt-10) REVERT: B 612 TYR cc_start: 0.9082 (m-80) cc_final: 0.8630 (m-80) REVERT: B 624 PHE cc_start: 0.9169 (m-80) cc_final: 0.8746 (m-80) REVERT: C 85 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: C 96 MET cc_start: 0.7955 (mmm) cc_final: 0.7652 (mmt) REVERT: C 137 MET cc_start: 0.1103 (mtp) cc_final: 0.0842 (mmp) REVERT: D 56 MET cc_start: 0.2300 (ptp) cc_final: 0.1950 (tpt) outliers start: 69 outliers final: 21 residues processed: 350 average time/residue: 0.5932 time to fit residues: 231.3614 Evaluate side-chains 300 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 275 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 0.7980 chunk 167 optimal weight: 40.0000 chunk 189 optimal weight: 40.0000 chunk 193 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 668 ASN B 180 ASN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 128 ASN D 132 GLN D 146 GLN D 192 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.186662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100356 restraints weight = 22961.704| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.72 r_work: 0.2794 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2635 r_free = 0.2635 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17067 Z= 0.148 Angle : 0.558 10.719 23058 Z= 0.290 Chirality : 0.041 0.169 2468 Planarity : 0.003 0.041 2935 Dihedral : 8.886 128.455 2383 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.52 % Allowed : 18.15 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.18), residues: 2016 helix: 1.64 (0.15), residues: 1174 sheet: 0.35 (0.40), residues: 153 loop : 0.42 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 235 TYR 0.022 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.009 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (17066) covalent geometry : angle 0.55765 / 0.29 (23056) SS BOND : bond 0.00085 / 0.04 ( 1) SS BOND : angle 1.59433 / 0.84 ( 2) hydrogen bonds : bond 0.03974 / 2.52 ( 908) hydrogen bonds : angle 4.68751 / 3.38 ( 2676) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 306 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.9219 (m-30) cc_final: 0.8984 (m-30) REVERT: A 66 GLU cc_start: 0.8703 (tp30) cc_final: 0.8395 (tp30) REVERT: A 99 LYS cc_start: 0.9053 (mmtt) cc_final: 0.8800 (mmtp) REVERT: A 103 ASP cc_start: 0.9225 (m-30) cc_final: 0.8916 (m-30) REVERT: A 110 ASP cc_start: 0.9332 (OUTLIER) cc_final: 0.9127 (p0) REVERT: A 246 SER cc_start: 0.8177 (m) cc_final: 0.7848 (p) REVERT: A 270 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.7910 (OUTLIER) REVERT: A 362 ASP cc_start: 0.8747 (m-30) cc_final: 0.8492 (m-30) REVERT: A 384 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8628 (pp20) REVERT: A 393 SER cc_start: 0.9067 (m) cc_final: 0.8587 (t) REVERT: A 413 SER cc_start: 0.9480 (m) cc_final: 0.9258 (p) REVERT: A 445 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 446 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6472 (mmp-170) REVERT: A 686 ARG cc_start: 0.8319 (mtp85) cc_final: 0.8032 (mtp85) REVERT: B 112 LYS cc_start: 0.9236 (mtmm) cc_final: 0.8947 (mtmm) REVERT: B 139 GLU cc_start: 0.9264 (mt-10) cc_final: 0.9023 (mt-10) REVERT: B 231 ASP cc_start: 0.9136 (t0) cc_final: 0.8812 (t0) REVERT: B 235 ARG cc_start: 0.9054 (ttm-80) cc_final: 0.8582 (mtm-85) REVERT: B 274 ARG cc_start: 0.8270 (ttm-80) cc_final: 0.7920 (ttm110) REVERT: B 321 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8601 (tm-30) REVERT: B 335 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 384 GLU cc_start: 0.9403 (OUTLIER) cc_final: 0.8667 (pp20) REVERT: B 393 SER cc_start: 0.9146 (m) cc_final: 0.8757 (t) REVERT: B 420 MET cc_start: 0.9584 (mmm) cc_final: 0.9327 (mmm) REVERT: B 446 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.7956 (mmm-85) REVERT: B 483 GLU cc_start: 0.9110 (mp0) cc_final: 0.8720 (mp0) REVERT: B 603 GLU cc_start: 0.9017 (tt0) cc_final: 0.8506 (mt-10) REVERT: B 604 ARG cc_start: 0.8888 (mmt-90) cc_final: 0.8481 (mmt-90) REVERT: B 612 TYR cc_start: 0.9009 (m-80) cc_final: 0.8643 (m-80) REVERT: B 624 PHE cc_start: 0.9167 (m-80) cc_final: 0.8765 (m-80) REVERT: B 686 ARG cc_start: 0.8644 (mtp-110) cc_final: 0.8184 (mtp-110) REVERT: C 96 MET cc_start: 0.7818 (mmm) cc_final: 0.7514 (mmt) REVERT: C 123 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7935 (tp30) REVERT: C 204 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.5346 (p90) REVERT: D 105 TYR cc_start: -0.1487 (OUTLIER) cc_final: -0.1831 (p90) REVERT: D 146 GLN cc_start: 0.6811 (OUTLIER) cc_final: 0.6565 (mp10) outliers start: 63 outliers final: 24 residues processed: 344 average time/residue: 0.5803 time to fit residues: 222.3930 Evaluate side-chains 312 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 146 GLN Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 239 GLN A 668 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.187883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.100022 restraints weight = 22795.567| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.79 r_work: 0.2763 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2611 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2611 r_free = 0.2611 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17067 Z= 0.183 Angle : 0.583 10.098 23058 Z= 0.299 Chirality : 0.042 0.169 2468 Planarity : 0.003 0.041 2935 Dihedral : 8.624 129.723 2383 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.29 % Allowed : 19.43 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.18), residues: 2016 helix: 1.62 (0.15), residues: 1177 sheet: 0.16 (0.39), residues: 157 loop : 0.35 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.024 0.001 TYR D 105 PHE 0.015 0.001 PHE A 100 TRP 0.009 0.001 TRP B 9 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (17066) covalent geometry : angle 0.58323 / 0.30 (23056) SS BOND : bond 0.00175 / 0.09 ( 1) SS BOND : angle 1.40291 / 0.74 ( 2) hydrogen bonds : bond 0.03780 / 2.41 ( 908) hydrogen bonds : angle 4.64460 / 3.37 ( 2676) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.9205 (m-30) cc_final: 0.8995 (m-30) REVERT: A 66 GLU cc_start: 0.8731 (tp30) cc_final: 0.8355 (tp30) REVERT: A 99 LYS cc_start: 0.9056 (mmtt) cc_final: 0.8811 (mmtp) REVERT: A 103 ASP cc_start: 0.9205 (m-30) cc_final: 0.8929 (m-30) REVERT: A 194 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8992 (ttmm) REVERT: A 246 SER cc_start: 0.8231 (m) cc_final: 0.7889 (p) REVERT: A 270 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8007 (OUTLIER) REVERT: A 345 LYS cc_start: 0.9393 (OUTLIER) cc_final: 0.8703 (ttpt) REVERT: A 362 ASP cc_start: 0.8770 (m-30) cc_final: 0.8508 (m-30) REVERT: A 384 GLU cc_start: 0.9411 (OUTLIER) cc_final: 0.8587 (pp20) REVERT: A 393 SER cc_start: 0.9050 (m) cc_final: 0.8556 (t) REVERT: A 421 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8502 (tm-30) REVERT: A 445 ILE cc_start: 0.9319 (OUTLIER) cc_final: 0.8981 (mm) REVERT: A 686 ARG cc_start: 0.8355 (mtp85) cc_final: 0.8008 (mtp85) REVERT: B 112 LYS cc_start: 0.9271 (mtmm) cc_final: 0.9039 (mtmm) REVERT: B 274 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8026 (ttm110) REVERT: B 321 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 335 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 348 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8512 (tmm) REVERT: B 384 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9095 (pp20) REVERT: B 393 SER cc_start: 0.9134 (m) cc_final: 0.8788 (t) REVERT: B 420 MET cc_start: 0.9599 (mmm) cc_final: 0.9339 (mmm) REVERT: B 446 ARG cc_start: 0.8339 (mmm-85) cc_final: 0.8074 (mmm-85) REVERT: B 483 GLU cc_start: 0.9098 (mp0) cc_final: 0.8688 (mp0) REVERT: B 603 GLU cc_start: 0.9063 (tt0) cc_final: 0.8485 (mt-10) REVERT: B 604 ARG cc_start: 0.8906 (mmt-90) cc_final: 0.8432 (mmt-90) REVERT: B 610 LYS cc_start: 0.8968 (ttpp) cc_final: 0.8670 (ttmm) REVERT: B 612 TYR cc_start: 0.9001 (m-80) cc_final: 0.8596 (m-80) REVERT: B 624 PHE cc_start: 0.9201 (m-80) cc_final: 0.8783 (m-80) REVERT: B 686 ARG cc_start: 0.8675 (mtp-110) cc_final: 0.8241 (mtp-110) REVERT: C 85 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6408 (tm-30) REVERT: D 56 MET cc_start: 0.2399 (ptp) cc_final: 0.2015 (tpt) REVERT: D 105 TYR cc_start: -0.1410 (OUTLIER) cc_final: -0.1705 (p90) outliers start: 59 outliers final: 23 residues processed: 326 average time/residue: 0.5473 time to fit residues: 198.7149 Evaluate side-chains 306 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 98 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 174 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 163 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 116 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 154 optimal weight: 40.0000 chunk 101 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 668 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.187698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.100201 restraints weight = 22815.274| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.70 r_work: 0.2763 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17067 Z= 0.180 Angle : 0.587 12.209 23058 Z= 0.299 Chirality : 0.042 0.204 2468 Planarity : 0.003 0.046 2935 Dihedral : 8.398 130.941 2381 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.29 % Allowed : 19.77 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.18), residues: 2016 helix: 1.54 (0.15), residues: 1178 sheet: 0.14 (0.39), residues: 157 loop : 0.25 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 243 TYR 0.033 0.001 TYR C 204 PHE 0.015 0.001 PHE B 100 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.18 (17066) covalent geometry : angle 0.58730 / 0.30 (23056) SS BOND : bond 0.00148 / 0.08 ( 1) SS BOND : angle 1.25603 / 0.66 ( 2) hydrogen bonds : bond 0.03697 / 2.36 ( 908) hydrogen bonds : angle 4.61452 / 3.35 ( 2676) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 293 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8714 (tp30) cc_final: 0.8362 (tp30) REVERT: A 99 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8858 (mmtp) REVERT: A 103 ASP cc_start: 0.9205 (m-30) cc_final: 0.8941 (m-30) REVERT: A 110 ASP cc_start: 0.9306 (OUTLIER) cc_final: 0.8654 (p0) REVERT: A 246 SER cc_start: 0.8209 (m) cc_final: 0.7880 (p) REVERT: A 345 LYS cc_start: 0.9437 (OUTLIER) cc_final: 0.8740 (ttpt) REVERT: A 362 ASP cc_start: 0.8713 (m-30) cc_final: 0.8474 (m-30) REVERT: A 384 GLU cc_start: 0.9415 (OUTLIER) cc_final: 0.8613 (pp20) REVERT: A 393 SER cc_start: 0.9093 (m) cc_final: 0.8666 (t) REVERT: A 445 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.8983 (mm) REVERT: A 598 MET cc_start: 0.9360 (mtm) cc_final: 0.8811 (mtm) REVERT: A 677 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8734 (mmm160) REVERT: A 686 ARG cc_start: 0.8421 (mtp85) cc_final: 0.7945 (mtp85) REVERT: B 53 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8864 (mp0) REVERT: B 217 GLU cc_start: 0.9002 (mp0) cc_final: 0.8785 (mm-30) REVERT: B 231 ASP cc_start: 0.9221 (t0) cc_final: 0.9017 (t0) REVERT: B 235 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8811 (ttm-80) REVERT: B 274 ARG cc_start: 0.8421 (ttm-80) cc_final: 0.8067 (ttm110) REVERT: B 321 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8675 (tm-30) REVERT: B 335 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8227 (mt-10) REVERT: B 348 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8592 (tmm) REVERT: B 393 SER cc_start: 0.9157 (m) cc_final: 0.8815 (t) REVERT: B 420 MET cc_start: 0.9606 (mmm) cc_final: 0.9382 (mmm) REVERT: B 483 GLU cc_start: 0.9113 (mp0) cc_final: 0.8725 (mp0) REVERT: B 603 GLU cc_start: 0.9039 (tt0) cc_final: 0.8458 (mt-10) REVERT: B 604 ARG cc_start: 0.8954 (mmt-90) cc_final: 0.8454 (mmt-90) REVERT: B 610 LYS cc_start: 0.9020 (ttpp) cc_final: 0.8719 (ttmm) REVERT: B 612 TYR cc_start: 0.8989 (m-80) cc_final: 0.8612 (m-80) REVERT: B 624 PHE cc_start: 0.9236 (m-80) cc_final: 0.8820 (m-80) REVERT: B 686 ARG cc_start: 0.8663 (mtp-110) cc_final: 0.8271 (mtp-110) REVERT: C 85 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: C 146 GLN cc_start: 0.7263 (mm-40) cc_final: 0.6992 (mm-40) REVERT: D 56 MET cc_start: 0.2632 (ptp) cc_final: 0.2225 (tpt) REVERT: D 105 TYR cc_start: -0.1315 (OUTLIER) cc_final: -0.1598 (p90) REVERT: E 34 MET cc_start: 0.6397 (mtm) cc_final: 0.6114 (pp-130) outliers start: 59 outliers final: 24 residues processed: 326 average time/residue: 0.6502 time to fit residues: 235.7428 Evaluate side-chains 311 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 279 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 136 optimal weight: 30.0000 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 170 optimal weight: 40.0000 chunk 116 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** C 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.184600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.097110 restraints weight = 23083.873| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.85 r_work: 0.2711 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17067 Z= 0.260 Angle : 0.618 11.541 23058 Z= 0.318 Chirality : 0.043 0.204 2468 Planarity : 0.003 0.052 2935 Dihedral : 8.396 131.810 2379 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 3.24 % Allowed : 20.27 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.18), residues: 2016 helix: 1.51 (0.15), residues: 1179 sheet: 0.10 (0.39), residues: 157 loop : 0.24 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 350 TYR 0.033 0.002 TYR D 174 PHE 0.016 0.002 PHE D 154 TRP 0.008 0.001 TRP B 9 HIS 0.006 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.26 (17066) covalent geometry : angle 0.61824 / 0.32 (23056) SS BOND : bond 0.00126 / 0.07 ( 1) SS BOND : angle 1.16330 / 0.61 ( 2) hydrogen bonds : bond 0.03798 / 2.42 ( 908) hydrogen bonds : angle 4.67494 / 3.39 ( 2676) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASN cc_start: 0.9389 (m-40) cc_final: 0.8977 (m-40) REVERT: A 66 GLU cc_start: 0.8718 (tp30) cc_final: 0.8318 (tp30) REVERT: A 110 ASP cc_start: 0.9277 (OUTLIER) cc_final: 0.8694 (p0) REVERT: A 194 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8876 (ttmm) REVERT: A 246 SER cc_start: 0.8073 (m) cc_final: 0.7709 (p) REVERT: A 345 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8608 (ttpt) REVERT: A 362 ASP cc_start: 0.8770 (m-30) cc_final: 0.8495 (m-30) REVERT: A 384 GLU cc_start: 0.9472 (OUTLIER) cc_final: 0.8620 (pp20) REVERT: A 393 SER cc_start: 0.9083 (m) cc_final: 0.8587 (t) REVERT: A 439 VAL cc_start: 0.9330 (t) cc_final: 0.9052 (p) REVERT: A 445 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9085 (mm) REVERT: A 570 MET cc_start: 0.9440 (mtp) cc_final: 0.9164 (mtm) REVERT: A 598 MET cc_start: 0.9372 (mtm) cc_final: 0.8759 (mtm) REVERT: A 677 ARG cc_start: 0.9265 (OUTLIER) cc_final: 0.8793 (mmm160) REVERT: A 686 ARG cc_start: 0.8362 (mtp85) cc_final: 0.7807 (mtp85) REVERT: B 53 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9087 (tt0) REVERT: B 66 GLU cc_start: 0.8708 (tp30) cc_final: 0.8463 (tp30) REVERT: B 112 LYS cc_start: 0.9245 (mtmm) cc_final: 0.8984 (mtmm) REVERT: B 217 GLU cc_start: 0.9009 (mp0) cc_final: 0.8751 (mm-30) REVERT: B 274 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8014 (ttm110) REVERT: B 296 LYS cc_start: 0.8838 (mtpm) cc_final: 0.8589 (mtpp) REVERT: B 321 GLU cc_start: 0.8891 (tm-30) cc_final: 0.8538 (tm-30) REVERT: B 335 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 336 LYS cc_start: 0.9481 (OUTLIER) cc_final: 0.9000 (ttmm) REVERT: B 348 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8680 (tmm) REVERT: B 384 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.8803 (pp20) REVERT: B 393 SER cc_start: 0.9110 (m) cc_final: 0.8734 (t) REVERT: B 420 MET cc_start: 0.9603 (mmm) cc_final: 0.9401 (mmm) REVERT: B 446 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: B 483 GLU cc_start: 0.9106 (mp0) cc_final: 0.8663 (mp0) REVERT: B 603 GLU cc_start: 0.9107 (tt0) cc_final: 0.8317 (mt-10) REVERT: B 604 ARG cc_start: 0.8941 (mmt-90) cc_final: 0.8407 (mmt-90) REVERT: B 610 LYS cc_start: 0.8982 (ttpp) cc_final: 0.8682 (ttpp) REVERT: B 612 TYR cc_start: 0.9052 (m-80) cc_final: 0.8509 (m-80) REVERT: B 624 PHE cc_start: 0.9306 (m-80) cc_final: 0.8881 (m-80) REVERT: B 686 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8140 (mtp-110) REVERT: C 85 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: C 146 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7044 (mm-40) REVERT: D 56 MET cc_start: 0.2587 (ptp) cc_final: 0.2164 (tpt) REVERT: D 105 TYR cc_start: -0.1283 (OUTLIER) cc_final: -0.1575 (p90) REVERT: E 34 MET cc_start: 0.6413 (mtm) cc_final: 0.6099 (pp-130) outliers start: 58 outliers final: 28 residues processed: 315 average time/residue: 0.6336 time to fit residues: 221.4328 Evaluate side-chains 304 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 98 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 159 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 118 optimal weight: 0.7980 chunk 183 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 143 optimal weight: 20.0000 chunk 80 optimal weight: 0.0870 chunk 67 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.186888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.101189 restraints weight = 23135.346| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.91 r_work: 0.2790 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17067 Z= 0.128 Angle : 0.580 12.131 23058 Z= 0.296 Chirality : 0.041 0.197 2468 Planarity : 0.003 0.053 2935 Dihedral : 8.040 132.437 2379 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.57 % Allowed : 21.05 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.18), residues: 2016 helix: 1.58 (0.15), residues: 1178 sheet: -0.25 (0.38), residues: 173 loop : 0.27 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.021 0.001 TYR D 105 PHE 0.016 0.001 PHE B 100 TRP 0.006 0.001 TRP B 9 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (17066) covalent geometry : angle 0.58029 / 0.30 (23056) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 1.05590 / 0.56 ( 2) hydrogen bonds : bond 0.03468 / 2.20 ( 908) hydrogen bonds : angle 4.56829 / 3.32 ( 2676) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 313 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9144 (t80) cc_final: 0.8890 (t80) REVERT: A 44 ASN cc_start: 0.9387 (m-40) cc_final: 0.8982 (m-40) REVERT: A 66 GLU cc_start: 0.8688 (tp30) cc_final: 0.8249 (tp30) REVERT: A 99 LYS cc_start: 0.8968 (mmtp) cc_final: 0.8611 (mmtt) REVERT: A 103 ASP cc_start: 0.9228 (m-30) cc_final: 0.8935 (m-30) REVERT: A 110 ASP cc_start: 0.9254 (OUTLIER) cc_final: 0.8673 (p0) REVERT: A 246 SER cc_start: 0.7945 (m) cc_final: 0.7656 (p) REVERT: A 286 ASP cc_start: 0.8961 (m-30) cc_final: 0.8172 (m-30) REVERT: A 362 ASP cc_start: 0.8759 (m-30) cc_final: 0.8137 (m-30) REVERT: A 384 GLU cc_start: 0.9412 (OUTLIER) cc_final: 0.8508 (pp20) REVERT: A 393 SER cc_start: 0.8985 (m) cc_final: 0.8546 (t) REVERT: A 439 VAL cc_start: 0.9246 (t) cc_final: 0.8995 (p) REVERT: A 445 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.8799 (mm) REVERT: A 570 MET cc_start: 0.9378 (mtp) cc_final: 0.9091 (mtm) REVERT: A 597 ILE cc_start: 0.9544 (pt) cc_final: 0.9305 (pp) REVERT: A 598 MET cc_start: 0.9388 (mtm) cc_final: 0.8832 (mtm) REVERT: A 677 ARG cc_start: 0.9266 (OUTLIER) cc_final: 0.8778 (mmm160) REVERT: A 686 ARG cc_start: 0.8338 (mtp85) cc_final: 0.7826 (mtp85) REVERT: B 53 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8834 (mp0) REVERT: B 66 GLU cc_start: 0.8655 (tp30) cc_final: 0.8381 (tp30) REVERT: B 112 LYS cc_start: 0.9206 (mtmm) cc_final: 0.8966 (mtmm) REVERT: B 274 ARG cc_start: 0.8413 (ttm-80) cc_final: 0.7976 (ttm110) REVERT: B 296 LYS cc_start: 0.8807 (mtpm) cc_final: 0.8584 (mtpp) REVERT: B 321 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 335 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8381 (mt-10) REVERT: B 348 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8613 (tmm) REVERT: B 393 SER cc_start: 0.9048 (m) cc_final: 0.8646 (t) REVERT: B 483 GLU cc_start: 0.9054 (mp0) cc_final: 0.8624 (mp0) REVERT: B 570 MET cc_start: 0.9616 (mtm) cc_final: 0.9358 (mtm) REVERT: B 603 GLU cc_start: 0.9049 (tt0) cc_final: 0.8321 (mt-10) REVERT: B 604 ARG cc_start: 0.8957 (mmt-90) cc_final: 0.8421 (mmt-90) REVERT: B 610 LYS cc_start: 0.9033 (ttpp) cc_final: 0.8703 (ttpp) REVERT: B 612 TYR cc_start: 0.8937 (m-80) cc_final: 0.8474 (m-80) REVERT: B 624 PHE cc_start: 0.9243 (m-80) cc_final: 0.8792 (m-80) REVERT: B 686 ARG cc_start: 0.8551 (mtp-110) cc_final: 0.8093 (mtp-110) REVERT: C 85 GLN cc_start: 0.6889 (OUTLIER) cc_final: 0.6336 (tm-30) REVERT: C 146 GLN cc_start: 0.7338 (mm-40) cc_final: 0.7056 (mm-40) REVERT: D 56 MET cc_start: 0.2505 (ptp) cc_final: 0.2086 (tpt) REVERT: D 74 MET cc_start: 0.3824 (OUTLIER) cc_final: 0.3382 (pmt) REVERT: D 105 TYR cc_start: -0.1242 (OUTLIER) cc_final: -0.1534 (p90) REVERT: E 34 MET cc_start: 0.6398 (mtm) cc_final: 0.6079 (pp-130) outliers start: 46 outliers final: 20 residues processed: 337 average time/residue: 0.5860 time to fit residues: 220.6861 Evaluate side-chains 312 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 284 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 189 optimal weight: 30.0000 chunk 106 optimal weight: 0.9990 chunk 182 optimal weight: 50.0000 chunk 144 optimal weight: 50.0000 chunk 180 optimal weight: 30.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN B 191 GLN B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.186242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.101528 restraints weight = 23350.681| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.88 r_work: 0.2786 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2623 r_free = 0.2623 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17067 Z= 0.170 Angle : 0.611 12.436 23058 Z= 0.310 Chirality : 0.042 0.214 2468 Planarity : 0.003 0.056 2935 Dihedral : 7.878 132.630 2379 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.57 % Allowed : 21.72 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.19), residues: 2016 helix: 1.56 (0.15), residues: 1178 sheet: -0.29 (0.38), residues: 173 loop : 0.25 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 235 TYR 0.022 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.008 0.001 TRP D 30 HIS 0.008 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (17066) covalent geometry : angle 0.61056 / 0.31 (23056) SS BOND : bond 0.00100 / 0.05 ( 1) SS BOND : angle 1.03746 / 0.55 ( 2) hydrogen bonds : bond 0.03534 / 2.23 ( 908) hydrogen bonds : angle 4.60610 / 3.36 ( 2676) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9200 (t80) cc_final: 0.8963 (t80) REVERT: A 44 ASN cc_start: 0.9459 (m-40) cc_final: 0.9063 (m-40) REVERT: A 66 GLU cc_start: 0.8599 (tp30) cc_final: 0.8248 (tp30) REVERT: A 99 LYS cc_start: 0.9166 (mmtp) cc_final: 0.8775 (mmtt) REVERT: A 103 ASP cc_start: 0.9185 (m-30) cc_final: 0.8928 (m-30) REVERT: A 110 ASP cc_start: 0.9290 (OUTLIER) cc_final: 0.8710 (p0) REVERT: A 194 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8930 (ttmm) REVERT: A 246 SER cc_start: 0.8141 (m) cc_final: 0.7831 (p) REVERT: A 270 ASP cc_start: 0.8637 (OUTLIER) cc_final: 0.8185 (OUTLIER) REVERT: A 274 ARG cc_start: 0.7864 (ptp-110) cc_final: 0.7433 (ttm-80) REVERT: A 318 ASP cc_start: 0.9015 (t0) cc_final: 0.8707 (t70) REVERT: A 362 ASP cc_start: 0.8728 (m-30) cc_final: 0.8486 (m-30) REVERT: A 384 GLU cc_start: 0.9447 (OUTLIER) cc_final: 0.9088 (pp20) REVERT: A 393 SER cc_start: 0.9125 (m) cc_final: 0.8699 (t) REVERT: A 413 SER cc_start: 0.9544 (OUTLIER) cc_final: 0.9343 (p) REVERT: A 439 VAL cc_start: 0.9401 (t) cc_final: 0.9145 (p) REVERT: A 445 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.8774 (mm) REVERT: A 446 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.6996 (mmp-170) REVERT: A 570 MET cc_start: 0.9407 (mtp) cc_final: 0.9075 (mtm) REVERT: A 677 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8724 (mmm160) REVERT: A 686 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8084 (mtp85) REVERT: B 66 GLU cc_start: 0.8602 (tp30) cc_final: 0.8374 (tp30) REVERT: B 112 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8974 (mtmm) REVERT: B 274 ARG cc_start: 0.8533 (ttm-80) cc_final: 0.8217 (ttm110) REVERT: B 296 LYS cc_start: 0.8922 (mtpm) cc_final: 0.8706 (mtpp) REVERT: B 321 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8591 (tm-30) REVERT: B 348 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8672 (tmm) REVERT: B 393 SER cc_start: 0.9129 (m) cc_final: 0.8737 (t) REVERT: B 483 GLU cc_start: 0.9119 (mp0) cc_final: 0.8731 (mp0) REVERT: B 570 MET cc_start: 0.9524 (OUTLIER) cc_final: 0.9320 (mtm) REVERT: B 603 GLU cc_start: 0.9008 (tt0) cc_final: 0.8301 (mt-10) REVERT: B 610 LYS cc_start: 0.9087 (ttpp) cc_final: 0.8821 (ttpp) REVERT: B 612 TYR cc_start: 0.8933 (m-80) cc_final: 0.8387 (m-80) REVERT: B 624 PHE cc_start: 0.9274 (m-80) cc_final: 0.8842 (m-80) REVERT: B 686 ARG cc_start: 0.8611 (mtp-110) cc_final: 0.8268 (mtm110) REVERT: C 85 GLN cc_start: 0.6895 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: C 146 GLN cc_start: 0.7402 (mm-40) cc_final: 0.7071 (mm-40) REVERT: D 56 MET cc_start: 0.2330 (ptp) cc_final: 0.1919 (tpt) REVERT: D 74 MET cc_start: 0.3283 (OUTLIER) cc_final: 0.2880 (pmt) REVERT: D 105 TYR cc_start: -0.1033 (OUTLIER) cc_final: -0.1344 (p90) REVERT: E 34 MET cc_start: 0.6432 (mtm) cc_final: 0.6095 (pp-130) outliers start: 46 outliers final: 24 residues processed: 313 average time/residue: 0.5362 time to fit residues: 186.4574 Evaluate side-chains 310 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 274 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 164 optimal weight: 6.9990 chunk 198 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 172 optimal weight: 50.0000 chunk 77 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.188340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.102450 restraints weight = 23160.720| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 2.89 r_work: 0.2778 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17067 Z= 0.184 Angle : 0.630 13.306 23058 Z= 0.319 Chirality : 0.043 0.235 2468 Planarity : 0.003 0.057 2935 Dihedral : 7.751 132.916 2379 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.40 % Allowed : 22.00 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 2016 helix: 1.52 (0.15), residues: 1178 sheet: -0.32 (0.38), residues: 173 loop : 0.26 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 235 TYR 0.022 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.008 0.001 TRP D 30 HIS 0.006 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 (17066) covalent geometry : angle 0.62976 / 0.32 (23056) SS BOND : bond 0.00090 / 0.05 ( 1) SS BOND : angle 0.99578 / 0.52 ( 2) hydrogen bonds : bond 0.03602 / 2.26 ( 908) hydrogen bonds : angle 4.63882 / 3.38 ( 2676) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 281 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9203 (t80) cc_final: 0.8950 (t80) REVERT: A 44 ASN cc_start: 0.9454 (m-40) cc_final: 0.9040 (m-40) REVERT: A 66 GLU cc_start: 0.8587 (tp30) cc_final: 0.8251 (tp30) REVERT: A 99 LYS cc_start: 0.9182 (mmtp) cc_final: 0.8798 (mmtt) REVERT: A 103 ASP cc_start: 0.9187 (m-30) cc_final: 0.8924 (m-30) REVERT: A 110 ASP cc_start: 0.9309 (OUTLIER) cc_final: 0.8688 (p0) REVERT: A 194 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8922 (ttmm) REVERT: A 246 SER cc_start: 0.8143 (m) cc_final: 0.7819 (p) REVERT: A 270 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8266 (OUTLIER) REVERT: A 276 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8744 (mmtt) REVERT: A 286 ASP cc_start: 0.9004 (m-30) cc_final: 0.8267 (m-30) REVERT: A 362 ASP cc_start: 0.8759 (m-30) cc_final: 0.8233 (m-30) REVERT: A 384 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.8634 (pp20) REVERT: A 393 SER cc_start: 0.9098 (m) cc_final: 0.8685 (t) REVERT: A 439 VAL cc_start: 0.9417 (t) cc_final: 0.9154 (p) REVERT: A 445 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.8825 (mm) REVERT: A 446 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7095 (mmp-170) REVERT: A 570 MET cc_start: 0.9425 (mtp) cc_final: 0.9095 (mtm) REVERT: A 677 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8723 (mmm160) REVERT: A 686 ARG cc_start: 0.8507 (mtp85) cc_final: 0.8209 (mtp-110) REVERT: B 66 GLU cc_start: 0.8595 (tp30) cc_final: 0.8389 (tp30) REVERT: B 112 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8982 (mtmm) REVERT: B 274 ARG cc_start: 0.8521 (ttm-80) cc_final: 0.8199 (ttm110) REVERT: B 296 LYS cc_start: 0.8920 (mtpm) cc_final: 0.8706 (mtpp) REVERT: B 321 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8583 (tm-30) REVERT: B 348 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8641 (tmm) REVERT: B 352 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8576 (mt-10) REVERT: B 393 SER cc_start: 0.9135 (m) cc_final: 0.8763 (t) REVERT: B 483 GLU cc_start: 0.9120 (mp0) cc_final: 0.8730 (mp0) REVERT: B 603 GLU cc_start: 0.9008 (tt0) cc_final: 0.8314 (mt-10) REVERT: B 610 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8798 (ttpp) REVERT: B 612 TYR cc_start: 0.8945 (m-80) cc_final: 0.8399 (m-80) REVERT: B 624 PHE cc_start: 0.9277 (m-80) cc_final: 0.8853 (m-80) REVERT: B 686 ARG cc_start: 0.8606 (mtp-110) cc_final: 0.8198 (mtp-110) REVERT: C 85 GLN cc_start: 0.6793 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: C 146 GLN cc_start: 0.7417 (mm-40) cc_final: 0.7111 (mm-40) REVERT: D 56 MET cc_start: 0.2366 (ptp) cc_final: 0.1930 (tpt) REVERT: D 74 MET cc_start: 0.3834 (OUTLIER) cc_final: 0.3449 (pmt) REVERT: D 105 TYR cc_start: -0.0845 (OUTLIER) cc_final: -0.1148 (p90) REVERT: E 34 MET cc_start: 0.6426 (mtm) cc_final: 0.6089 (pp-130) outliers start: 43 outliers final: 23 residues processed: 303 average time/residue: 0.6103 time to fit residues: 205.2905 Evaluate side-chains 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 275 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 194 optimal weight: 6.9990 chunk 148 optimal weight: 50.0000 chunk 57 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 189 optimal weight: 50.0000 chunk 186 optimal weight: 6.9990 chunk 82 optimal weight: 0.5980 chunk 163 optimal weight: 9.9990 chunk 156 optimal weight: 0.0050 chunk 114 optimal weight: 2.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.099147 restraints weight = 23327.575| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 2.90 r_work: 0.2747 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17067 Z= 0.223 Angle : 0.654 13.183 23058 Z= 0.332 Chirality : 0.044 0.244 2468 Planarity : 0.003 0.056 2935 Dihedral : 7.766 133.060 2379 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.35 % Allowed : 22.33 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.19), residues: 2016 helix: 1.49 (0.15), residues: 1174 sheet: -0.39 (0.37), residues: 173 loop : 0.24 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 235 TYR 0.022 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.008 0.001 TRP B 9 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (17066) covalent geometry : angle 0.65434 / 0.33 (23056) SS BOND : bond 0.00099 / 0.05 ( 1) SS BOND : angle 0.99639 / 0.53 ( 2) hydrogen bonds : bond 0.03671 / 2.30 ( 908) hydrogen bonds : angle 4.72593 / 3.44 ( 2676) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 286 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9199 (t80) cc_final: 0.8930 (t80) REVERT: A 44 ASN cc_start: 0.9449 (m-40) cc_final: 0.9034 (m-40) REVERT: A 66 GLU cc_start: 0.8630 (tp30) cc_final: 0.8287 (tp30) REVERT: A 99 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8813 (mmtt) REVERT: A 103 ASP cc_start: 0.9232 (m-30) cc_final: 0.8956 (m-30) REVERT: A 110 ASP cc_start: 0.9324 (OUTLIER) cc_final: 0.8701 (p0) REVERT: A 194 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8875 (ttmm) REVERT: A 246 SER cc_start: 0.8072 (m) cc_final: 0.7734 (p) REVERT: A 276 LYS cc_start: 0.9132 (mtpp) cc_final: 0.8797 (mmtt) REVERT: A 312 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8892 (pt0) REVERT: A 345 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.8694 (ttpt) REVERT: A 362 ASP cc_start: 0.8796 (m-30) cc_final: 0.8535 (m-30) REVERT: A 384 GLU cc_start: 0.9436 (OUTLIER) cc_final: 0.9034 (pp20) REVERT: A 393 SER cc_start: 0.9076 (m) cc_final: 0.8650 (t) REVERT: A 445 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.8960 (mm) REVERT: A 446 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7146 (mmp-170) REVERT: A 570 MET cc_start: 0.9468 (mtp) cc_final: 0.9113 (mtm) REVERT: A 677 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8763 (mmm160) REVERT: A 686 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8162 (mtp-110) REVERT: B 66 GLU cc_start: 0.8682 (tp30) cc_final: 0.8466 (tp30) REVERT: B 112 LYS cc_start: 0.9236 (mtmm) cc_final: 0.8978 (mtmm) REVERT: B 235 ARG cc_start: 0.9063 (ttp-110) cc_final: 0.8818 (ttm-80) REVERT: B 274 ARG cc_start: 0.8450 (ttm-80) cc_final: 0.8116 (ttm110) REVERT: B 296 LYS cc_start: 0.9009 (mtpm) cc_final: 0.8806 (mtpp) REVERT: B 321 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8657 (tm-30) REVERT: B 348 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8783 (tmm) REVERT: B 393 SER cc_start: 0.9117 (m) cc_final: 0.8725 (t) REVERT: B 483 GLU cc_start: 0.9135 (mp0) cc_final: 0.8753 (mp0) REVERT: B 570 MET cc_start: 0.9594 (mtm) cc_final: 0.9390 (mtm) REVERT: B 603 GLU cc_start: 0.9054 (tt0) cc_final: 0.8360 (mt-10) REVERT: B 610 LYS cc_start: 0.9046 (ttpp) cc_final: 0.8688 (ttpp) REVERT: B 612 TYR cc_start: 0.8982 (m-80) cc_final: 0.8436 (m-80) REVERT: B 624 PHE cc_start: 0.9304 (m-80) cc_final: 0.8845 (m-80) REVERT: B 686 ARG cc_start: 0.8605 (mtp-110) cc_final: 0.8157 (mtp-110) REVERT: C 85 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.6179 (tm-30) REVERT: D 56 MET cc_start: 0.2353 (ptp) cc_final: 0.1919 (tpt) REVERT: D 74 MET cc_start: 0.3891 (OUTLIER) cc_final: 0.3458 (pmt) REVERT: D 105 TYR cc_start: -0.0852 (OUTLIER) cc_final: -0.1160 (p90) REVERT: D 319 ASP cc_start: 0.9042 (m-30) cc_final: 0.8312 (m-30) REVERT: E 34 MET cc_start: 0.6417 (mtm) cc_final: 0.6040 (pp-130) outliers start: 42 outliers final: 22 residues processed: 310 average time/residue: 0.5887 time to fit residues: 202.6707 Evaluate side-chains 310 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 276 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 165 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 179 optimal weight: 40.0000 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 43 optimal weight: 0.9980 chunk 160 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 218 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 668 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.185640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.104622 restraints weight = 23059.030| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.70 r_work: 0.2798 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17067 Z= 0.172 Angle : 0.634 12.864 23058 Z= 0.321 Chirality : 0.043 0.246 2468 Planarity : 0.003 0.056 2935 Dihedral : 7.600 133.487 2379 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.35 % Allowed : 22.61 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.19), residues: 2016 helix: 1.54 (0.15), residues: 1168 sheet: -0.43 (0.37), residues: 173 loop : 0.30 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 235 TYR 0.021 0.001 TYR D 105 PHE 0.016 0.001 PHE A 100 TRP 0.007 0.001 TRP B 9 HIS 0.006 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (17066) covalent geometry : angle 0.63433 / 0.32 (23056) SS BOND : bond 0.00087 / 0.05 ( 1) SS BOND : angle 0.96520 / 0.51 ( 2) hydrogen bonds : bond 0.03584 / 2.23 ( 908) hydrogen bonds : angle 4.67508 / 3.40 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9420.32 seconds wall clock time: 160 minutes 26.32 seconds (9626.32 seconds total)