Starting phenix.real_space_refine on Fri Jul 3 22:10:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byl_45037/07_2026/9byl_45037_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byl_45037/07_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_45037/07_2026/9byl_45037_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byl_45037/07_2026/9byl_45037_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byl_45037/07_2026/9byl_45037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byl_45037/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 3.70, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 930.0 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: 2.99 Time building geometry restraints manager: 1.58 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 3.060 ... (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: 1.660 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.150 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.170 ------------------------------------------------------------------------------- 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 : 0.563 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: 0.5765 time to fit residues: 315.6729 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 : 0.659 ------------------------------------------------------------------------------- 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 201 HIS 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 201 HIS ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.186407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098038 restraints weight = 22771.865| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 2.79 r_work: 0.2762 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 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 = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17067 Z= 0.205 Angle : 0.617 12.595 23058 Z= 0.322 Chirality : 0.043 0.212 2468 Planarity : 0.003 0.040 2935 Dihedral : 9.436 126.998 2393 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 3.80 % Allowed : 18.15 % Favored : 78.06 % 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: 1.68 (0.18), residues: 2016 helix: 1.62 (0.15), residues: 1165 sheet: 0.37 (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 0.021 0.001 TYR C 213 PHE 0.017 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 0.00458 / 0.20 (17066) covalent geometry : angle 0.61642 / 0.32 (23056) SS BOND : bond 0.00830 / 0.44 ( 1) SS BOND : angle 1.96208 / 1.04 ( 2) hydrogen bonds : bond 0.04739 / 2.98 ( 908) hydrogen bonds : angle 4.98014 / 3.58 ( 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: 68 poor density : 309 time to evaluate : 0.675 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 39 ASP cc_start: 0.9239 (m-30) cc_final: 0.8989 (m-30) REVERT: A 66 GLU cc_start: 0.8699 (tp30) cc_final: 0.8356 (tp30) REVERT: A 99 LYS cc_start: 0.8954 (mmtt) cc_final: 0.8745 (mmtp) REVERT: A 103 ASP cc_start: 0.9211 (m-30) cc_final: 0.8849 (m-30) REVERT: A 110 ASP cc_start: 0.9341 (OUTLIER) cc_final: 0.8550 (p0) REVERT: A 194 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8863 (ttmm) REVERT: A 246 SER cc_start: 0.8136 (m) cc_final: 0.7753 (p) REVERT: A 270 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.7909 (OUTLIER) REVERT: A 274 ARG cc_start: 0.8319 (ptp-110) cc_final: 0.8061 (ptp-110) REVERT: A 286 ASP cc_start: 0.8942 (m-30) cc_final: 0.8386 (m-30) REVERT: A 362 ASP cc_start: 0.8683 (m-30) cc_final: 0.8298 (m-30) REVERT: A 384 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: A 421 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8462 (tm-30) REVERT: A 459 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8961 (mttm) REVERT: A 583 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9133 (t) REVERT: A 686 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7961 (mtp85) REVERT: B 104 TYR cc_start: 0.9145 (m-80) cc_final: 0.8829 (m-80) REVERT: B 112 LYS cc_start: 0.9297 (mtmm) cc_final: 0.9068 (mtmm) REVERT: B 139 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8952 (mt-10) REVERT: B 274 ARG cc_start: 0.8180 (ttm-80) cc_final: 0.7860 (ttm110) REVERT: B 321 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 483 GLU cc_start: 0.9060 (mp0) cc_final: 0.8618 (mp0) REVERT: B 603 GLU cc_start: 0.9076 (tt0) cc_final: 0.8314 (mt-10) REVERT: B 612 TYR cc_start: 0.9090 (m-80) cc_final: 0.8549 (m-80) REVERT: B 624 PHE cc_start: 0.9162 (m-80) cc_final: 0.8740 (m-80) REVERT: C 66 ASP cc_start: -0.0864 (OUTLIER) cc_final: -0.1452 (t0) REVERT: C 96 MET cc_start: 0.7957 (mmm) cc_final: 0.7700 (mmt) REVERT: C 123 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8000 (tp30) REVERT: C 137 MET cc_start: 0.1134 (mtp) cc_final: 0.0844 (mmp) REVERT: D 56 MET cc_start: 0.2151 (ptp) cc_final: 0.1810 (tpt) REVERT: D 235 LEU cc_start: 0.7654 (mt) cc_final: 0.7443 (pp) outliers start: 68 outliers final: 21 residues processed: 352 average time/residue: 0.5617 time to fit residues: 220.4980 Evaluate side-chains 299 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 272 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 459 LYS Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 583 SER 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 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 66 ASP 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: 0.5980 chunk 167 optimal weight: 40.0000 chunk 189 optimal weight: 50.0000 chunk 193 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 ASN A 668 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 132 GLN D 146 GLN D 192 ASN D 238 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.189105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102692 restraints weight = 23200.105| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.82 r_work: 0.2796 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 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 = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17067 Z= 0.140 Angle : 0.565 10.656 23058 Z= 0.292 Chirality : 0.041 0.172 2468 Planarity : 0.003 0.041 2935 Dihedral : 8.933 128.165 2383 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.46 % Allowed : 18.03 % Favored : 78.50 % 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: 1.66 (0.15), residues: 1173 sheet: 0.35 (0.40), residues: 153 loop : 0.38 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.021 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.009 0.001 TRP D 30 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (17066) covalent geometry : angle 0.56522 / 0.29 (23056) SS BOND : bond 0.00144 / 0.08 ( 1) SS BOND : angle 1.57635 / 0.83 ( 2) hydrogen bonds : bond 0.04049 / 2.57 ( 908) hydrogen bonds : angle 4.71702 / 3.40 ( 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: 62 poor density : 307 time to evaluate : 0.656 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 8 LYS cc_start: 0.9323 (tttt) cc_final: 0.9117 (tttp) REVERT: A 39 ASP cc_start: 0.9214 (m-30) cc_final: 0.9001 (m-30) REVERT: A 66 GLU cc_start: 0.8691 (tp30) cc_final: 0.8387 (tp30) REVERT: A 99 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8872 (mmtp) REVERT: A 103 ASP cc_start: 0.9212 (m-30) cc_final: 0.8914 (m-30) REVERT: A 194 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9119 (ttmm) REVERT: A 246 SER cc_start: 0.8235 (m) cc_final: 0.7922 (p) REVERT: A 270 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.7979 (OUTLIER) REVERT: A 286 ASP cc_start: 0.8964 (m-30) cc_final: 0.8445 (m-30) REVERT: A 362 ASP cc_start: 0.8726 (m-30) cc_final: 0.8374 (m-30) REVERT: A 384 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8680 (pp20) REVERT: A 393 SER cc_start: 0.9043 (m) cc_final: 0.8610 (t) REVERT: A 446 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6857 (mmp-170) REVERT: A 493 MET cc_start: 0.9556 (tmm) cc_final: 0.9339 (tmm) REVERT: A 583 SER cc_start: 0.9516 (OUTLIER) cc_final: 0.9299 (t) REVERT: A 686 ARG cc_start: 0.8363 (mtp85) cc_final: 0.8006 (mtp85) REVERT: B 139 GLU cc_start: 0.9282 (mt-10) cc_final: 0.9027 (mt-10) REVERT: B 231 ASP cc_start: 0.9153 (t0) cc_final: 0.8916 (t0) REVERT: B 235 ARG cc_start: 0.9129 (ttm-80) cc_final: 0.8682 (mtm-85) REVERT: B 274 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8002 (ttm110) REVERT: B 321 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8565 (tm-30) REVERT: B 335 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8253 (mt-10) REVERT: B 384 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: B 393 SER cc_start: 0.9200 (m) cc_final: 0.8839 (t) REVERT: B 446 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7988 (mmm-85) REVERT: B 483 GLU cc_start: 0.9115 (mp0) cc_final: 0.8757 (mp0) REVERT: B 603 GLU cc_start: 0.9004 (tt0) cc_final: 0.8490 (mt-10) REVERT: B 612 TYR cc_start: 0.8993 (m-80) cc_final: 0.8605 (m-80) REVERT: B 624 PHE cc_start: 0.9140 (m-80) cc_final: 0.8779 (m-80) REVERT: B 686 ARG cc_start: 0.8678 (mtp-110) cc_final: 0.8212 (mtp-110) REVERT: C 85 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: C 96 MET cc_start: 0.7868 (mmm) cc_final: 0.7565 (mmt) REVERT: C 123 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7972 (tp30) REVERT: D 56 MET cc_start: 0.2203 (ptp) cc_final: 0.1756 (tpt) REVERT: D 105 TYR cc_start: -0.1521 (OUTLIER) cc_final: -0.1890 (p90) REVERT: D 146 GLN cc_start: 0.6650 (OUTLIER) cc_final: 0.6389 (mp10) outliers start: 62 outliers final: 23 residues processed: 345 average time/residue: 0.6191 time to fit residues: 237.4867 Evaluate side-chains 316 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 583 SER 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 C residue 85 GLN 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 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 146 GLN 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: 0.9980 chunk 132 optimal weight: 0.4980 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 136 optimal weight: 40.0000 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 668 ASN ** B 180 ASN ** 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** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.188843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.101633 restraints weight = 22996.541| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.72 r_work: 0.2795 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2633 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.076 | | 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) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17067 Z= 0.147 Angle : 0.574 11.393 23058 Z= 0.294 Chirality : 0.041 0.168 2468 Planarity : 0.003 0.043 2935 Dihedral : 8.500 129.309 2381 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.41 % Allowed : 19.71 % Favored : 76.88 % 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: 1.57 (0.18), residues: 2016 helix: 1.64 (0.15), residues: 1173 sheet: 0.19 (0.39), residues: 153 loop : 0.37 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 350 TYR 0.025 0.001 TYR D 105 PHE 0.014 0.001 PHE B 100 TRP 0.008 0.001 TRP B 9 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (17066) covalent geometry : angle 0.57408 / 0.29 (23056) SS BOND : bond 0.00173 / 0.09 ( 1) SS BOND : angle 1.36888 / 0.72 ( 2) hydrogen bonds : bond 0.03779 / 2.40 ( 908) hydrogen bonds : angle 4.64699 / 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 358 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 297 time to evaluate : 0.654 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 66 GLU cc_start: 0.8716 (tp30) cc_final: 0.8412 (tp30) REVERT: A 99 LYS cc_start: 0.9070 (mmtt) cc_final: 0.8782 (mmtp) REVERT: A 103 ASP cc_start: 0.9214 (m-30) cc_final: 0.8975 (m-30) REVERT: A 194 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9049 (ttmm) REVERT: A 246 SER cc_start: 0.8261 (m) cc_final: 0.7936 (p) REVERT: A 345 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.8755 (ttpt) REVERT: A 362 ASP cc_start: 0.8736 (m-30) cc_final: 0.8489 (m-30) REVERT: A 384 GLU cc_start: 0.9406 (OUTLIER) cc_final: 0.8638 (pp20) REVERT: A 393 SER cc_start: 0.9058 (m) cc_final: 0.8614 (t) REVERT: A 421 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8496 (pp20) REVERT: A 445 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8695 (mm) REVERT: A 446 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6731 (mmp-170) REVERT: A 493 MET cc_start: 0.9570 (tmm) cc_final: 0.9369 (tmm) REVERT: A 583 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9306 (t) REVERT: A 598 MET cc_start: 0.9380 (mtm) cc_final: 0.9129 (mtm) REVERT: B 221 LYS cc_start: 0.9344 (mttm) cc_final: 0.9141 (mttm) REVERT: B 274 ARG cc_start: 0.8353 (ttm-80) cc_final: 0.7986 (ttm110) REVERT: B 318 ASP cc_start: 0.8757 (t0) cc_final: 0.8512 (t0) REVERT: B 321 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8577 (tm-30) REVERT: B 335 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8271 (mt-10) REVERT: B 384 GLU cc_start: 0.9336 (OUTLIER) cc_final: 0.8974 (pp20) REVERT: B 393 SER cc_start: 0.9155 (m) cc_final: 0.8803 (t) REVERT: B 446 ARG cc_start: 0.8278 (mmm-85) cc_final: 0.8016 (mmm-85) REVERT: B 483 GLU cc_start: 0.9115 (mp0) cc_final: 0.8736 (mp0) REVERT: B 603 GLU cc_start: 0.9047 (tt0) cc_final: 0.8553 (mt-10) REVERT: B 612 TYR cc_start: 0.8966 (m-80) cc_final: 0.8595 (m-80) REVERT: B 624 PHE cc_start: 0.9180 (m-80) cc_final: 0.8804 (m-80) REVERT: B 686 ARG cc_start: 0.8654 (mtp-110) cc_final: 0.8089 (mtp-110) REVERT: C 85 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6557 (tm-30) REVERT: C 123 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7881 (tp30) REVERT: D 105 TYR cc_start: -0.1410 (OUTLIER) cc_final: -0.1694 (p90) outliers start: 61 outliers final: 25 residues processed: 330 average time/residue: 0.6380 time to fit residues: 233.0839 Evaluate side-chains 312 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 267 ILE 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 583 SER 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 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 194 ILE 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: 0.8980 chunk 163 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 194 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 154 optimal weight: 30.0000 chunk 101 optimal weight: 0.5980 chunk 158 optimal weight: 9.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 GLN A 668 ASN B 180 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** B 410 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.184755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.101765 restraints weight = 22924.639| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 2.56 r_work: 0.2730 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 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 = 0.2576 r_free = 0.2576 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: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3391 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= 0.257 Angle : 0.623 10.795 23058 Z= 0.321 Chirality : 0.043 0.202 2468 Planarity : 0.003 0.051 2935 Dihedral : 8.564 130.846 2381 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.35 % Allowed : 19.93 % Favored : 76.72 % 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: 1.53 (0.15), residues: 1180 sheet: 0.09 (0.39), residues: 157 loop : 0.25 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.026 0.002 TYR D 174 PHE 0.016 0.002 PHE A 487 TRP 0.009 0.001 TRP B 9 HIS 0.009 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00581 / 0.26 (17066) covalent geometry : angle 0.62337 / 0.32 (23056) SS BOND : bond 0.00154 / 0.08 ( 1) SS BOND : angle 1.24788 / 0.66 ( 2) hydrogen bonds : bond 0.03930 / 2.50 ( 908) hydrogen bonds : angle 4.71949 / 3.42 ( 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 345 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 285 time to evaluate : 0.701 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 66 GLU cc_start: 0.8725 (tp30) cc_final: 0.8397 (tp30) REVERT: A 99 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8910 (mmtp) REVERT: A 103 ASP cc_start: 0.9233 (m-30) cc_final: 0.8914 (m-30) REVERT: A 110 ASP cc_start: 0.9419 (OUTLIER) cc_final: 0.8722 (p0) REVERT: A 119 GLU cc_start: 0.9245 (mp0) cc_final: 0.9040 (mp0) REVERT: A 194 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9020 (ttmm) REVERT: A 246 SER cc_start: 0.8249 (m) cc_final: 0.7892 (p) REVERT: A 345 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8711 (ttpt) REVERT: A 362 ASP cc_start: 0.8756 (m-30) cc_final: 0.8513 (m-30) REVERT: A 384 GLU cc_start: 0.9457 (OUTLIER) cc_final: 0.9130 (pp20) REVERT: A 393 SER cc_start: 0.9086 (m) cc_final: 0.8646 (t) REVERT: A 445 ILE cc_start: 0.9406 (OUTLIER) cc_final: 0.9059 (mm) REVERT: A 583 SER cc_start: 0.9551 (t) cc_final: 0.9293 (t) REVERT: A 677 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8749 (mmm160) REVERT: A 686 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8149 (mtp-110) REVERT: B 53 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8825 (mm-30) REVERT: B 104 TYR cc_start: 0.9157 (m-80) cc_final: 0.8640 (m-80) REVERT: B 217 GLU cc_start: 0.8985 (mp0) cc_final: 0.8760 (mm-30) REVERT: B 235 ARG cc_start: 0.9260 (tpp80) cc_final: 0.9032 (ttm-80) REVERT: B 274 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8082 (ttm110) REVERT: B 318 ASP cc_start: 0.8883 (t0) cc_final: 0.8568 (t0) REVERT: B 321 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 335 GLU cc_start: 0.8504 (mt-10) cc_final: 0.8232 (mt-10) REVERT: B 336 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.8993 (ttmm) REVERT: B 348 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8574 (tmm) REVERT: B 384 GLU cc_start: 0.9430 (OUTLIER) cc_final: 0.8717 (pp20) REVERT: B 393 SER cc_start: 0.9139 (m) cc_final: 0.8774 (t) REVERT: B 483 GLU cc_start: 0.9130 (mp0) cc_final: 0.8706 (mp0) REVERT: B 603 GLU cc_start: 0.9074 (tt0) cc_final: 0.8483 (mt-10) REVERT: B 610 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8621 (ttmm) REVERT: B 612 TYR cc_start: 0.9051 (m-80) cc_final: 0.8648 (m-80) REVERT: B 624 PHE cc_start: 0.9236 (m-80) cc_final: 0.8799 (m-80) REVERT: B 686 ARG cc_start: 0.8658 (mtp-110) cc_final: 0.8291 (mtp-110) REVERT: C 85 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: D 56 MET cc_start: 0.2672 (ptp) cc_final: 0.2307 (tpt) REVERT: D 74 MET cc_start: 0.4695 (ttt) cc_final: 0.4480 (ptt) REVERT: D 105 TYR cc_start: -0.1376 (OUTLIER) cc_final: -0.1666 (p90) REVERT: E 34 MET cc_start: 0.6380 (mtm) cc_final: 0.6116 (pp-130) outliers start: 60 outliers final: 27 residues processed: 322 average time/residue: 0.6355 time to fit residues: 227.3114 Evaluate side-chains 307 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 348 MET 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 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 B residue 41 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 336 LYS 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 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 204 TYR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 98 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 170 optimal weight: 30.0000 chunk 116 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN C 127 GLN ** D 263 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 = 0.4101 r_free = 0.4101 target = 0.188369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101820 restraints weight = 23044.315| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.68 r_work: 0.2790 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 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 = 0.2636 r_free = 0.2636 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 (9 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17067 Z= 0.138 Angle : 0.582 11.405 23058 Z= 0.297 Chirality : 0.041 0.202 2468 Planarity : 0.003 0.055 2935 Dihedral : 8.277 131.853 2381 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.85 % Allowed : 20.66 % 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: 1.42 (0.18), residues: 2016 helix: 1.57 (0.15), residues: 1177 sheet: -0.01 (0.39), residues: 157 loop : 0.21 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.029 0.001 TYR D 174 PHE 0.015 0.001 PHE B 100 TRP 0.007 0.001 TRP A 9 HIS 0.003 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (17066) covalent geometry : angle 0.58152 / 0.30 (23056) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 1.11491 / 0.59 ( 2) hydrogen bonds : bond 0.03601 / 2.29 ( 908) hydrogen bonds : angle 4.59578 / 3.33 ( 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 358 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 307 time to evaluate : 0.467 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 44 ASN cc_start: 0.9433 (m-40) cc_final: 0.9045 (m-40) REVERT: A 66 GLU cc_start: 0.8681 (tp30) cc_final: 0.8339 (tp30) REVERT: A 99 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8816 (mmtp) REVERT: A 103 ASP cc_start: 0.9234 (m-30) cc_final: 0.9009 (m-30) REVERT: A 110 ASP cc_start: 0.9420 (OUTLIER) cc_final: 0.8728 (p0) REVERT: A 119 GLU cc_start: 0.9204 (mp0) cc_final: 0.8976 (mp0) REVERT: A 184 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8765 (tpp-160) REVERT: A 246 SER cc_start: 0.8121 (m) cc_final: 0.7852 (p) REVERT: A 286 ASP cc_start: 0.8989 (m-30) cc_final: 0.8199 (m-30) REVERT: A 362 ASP cc_start: 0.8772 (m-30) cc_final: 0.8174 (m-30) REVERT: A 384 GLU cc_start: 0.9371 (OUTLIER) cc_final: 0.8572 (pp20) REVERT: A 393 SER cc_start: 0.9102 (m) cc_final: 0.8703 (t) REVERT: A 413 SER cc_start: 0.9595 (OUTLIER) cc_final: 0.9333 (p) REVERT: A 421 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8485 (pp20) REVERT: A 445 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9015 (mm) REVERT: A 493 MET cc_start: 0.9562 (tmm) cc_final: 0.9290 (tmm) REVERT: A 570 MET cc_start: 0.9390 (mtm) cc_final: 0.9173 (mtm) REVERT: A 583 SER cc_start: 0.9547 (t) cc_final: 0.9342 (t) REVERT: A 677 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8717 (mmm160) REVERT: A 686 ARG cc_start: 0.8381 (mtp85) cc_final: 0.7961 (mtp85) REVERT: B 53 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8855 (mp0) REVERT: B 66 GLU cc_start: 0.8593 (tp30) cc_final: 0.8347 (tp30) REVERT: B 104 TYR cc_start: 0.9149 (m-80) cc_final: 0.8624 (m-80) REVERT: B 235 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8995 (ttm-80) REVERT: B 274 ARG cc_start: 0.8442 (ttm-80) cc_final: 0.8089 (ttm110) REVERT: B 296 LYS cc_start: 0.8887 (mtpm) cc_final: 0.8662 (mtpp) REVERT: B 318 ASP cc_start: 0.8893 (t0) cc_final: 0.8598 (t0) REVERT: B 321 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8567 (tm-30) REVERT: B 335 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8256 (mt-10) REVERT: B 348 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8601 (tmm) REVERT: B 393 SER cc_start: 0.9122 (m) cc_final: 0.8742 (t) REVERT: B 396 ASP cc_start: 0.9045 (m-30) cc_final: 0.8795 (m-30) REVERT: B 483 GLU cc_start: 0.9130 (mp0) cc_final: 0.8760 (mp0) REVERT: B 570 MET cc_start: 0.9587 (mtm) cc_final: 0.9357 (mtm) REVERT: B 603 GLU cc_start: 0.9027 (tt0) cc_final: 0.8328 (mt-10) REVERT: B 610 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8797 (ttpp) REVERT: B 612 TYR cc_start: 0.8963 (m-80) cc_final: 0.8496 (m-80) REVERT: B 624 PHE cc_start: 0.9230 (m-80) cc_final: 0.8826 (m-80) REVERT: B 686 ARG cc_start: 0.8661 (mtp-110) cc_final: 0.8326 (mtp-110) REVERT: C 68 GLU cc_start: 0.3685 (mm-30) cc_final: 0.2978 (pt0) REVERT: C 85 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.6470 (tm-30) REVERT: D 56 MET cc_start: 0.2440 (ptp) cc_final: 0.2002 (tpt) REVERT: D 105 TYR cc_start: -0.1293 (OUTLIER) cc_final: -0.1575 (p90) REVERT: E 34 MET cc_start: 0.6397 (mtm) cc_final: 0.6126 (pp-130) outliers start: 51 outliers final: 21 residues processed: 335 average time/residue: 0.5704 time to fit residues: 213.0829 Evaluate side-chains 309 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 280 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 277 THR Chi-restraints excluded: chain A residue 348 MET 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 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 B residue 216 VAL Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 MET 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 B residue 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 159 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 183 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 187 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098584 restraints weight = 23227.188| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.83 r_work: 0.2748 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 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 = 0.2592 r_free = 0.2592 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 (19 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17067 Z= 0.199 Angle : 0.608 11.902 23058 Z= 0.311 Chirality : 0.043 0.207 2468 Planarity : 0.003 0.057 2935 Dihedral : 8.173 132.249 2379 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.57 % Allowed : 21.38 % Favored : 76.05 % 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: 1.32 (0.18), residues: 2016 helix: 1.47 (0.15), residues: 1178 sheet: -0.19 (0.37), residues: 165 loop : 0.25 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.023 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.008 0.001 TRP D 30 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 (17066) covalent geometry : angle 0.60821 / 0.31 (23056) SS BOND : bond 0.00114 / 0.06 ( 1) SS BOND : angle 1.07587 / 0.57 ( 2) hydrogen bonds : bond 0.03699 / 2.34 ( 908) hydrogen bonds : angle 4.67725 / 3.39 ( 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 326 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 280 time to evaluate : 0.781 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: 0.9110 (t80) cc_final: 0.8887 (t80) REVERT: A 44 ASN cc_start: 0.9418 (m-40) cc_final: 0.8983 (m-40) REVERT: A 66 GLU cc_start: 0.8667 (tp30) cc_final: 0.8234 (tp30) REVERT: A 99 LYS cc_start: 0.8982 (mmtt) cc_final: 0.8710 (mmtp) REVERT: A 103 ASP cc_start: 0.9249 (m-30) cc_final: 0.8935 (m-30) REVERT: A 110 ASP cc_start: 0.9433 (OUTLIER) cc_final: 0.8739 (p0) REVERT: A 119 GLU cc_start: 0.9187 (mp0) cc_final: 0.8958 (mp0) REVERT: A 194 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8861 (ttmm) REVERT: A 246 SER cc_start: 0.8008 (m) cc_final: 0.7687 (p) REVERT: A 274 ARG cc_start: 0.8055 (ptp-110) cc_final: 0.7767 (ttm110) REVERT: A 286 ASP cc_start: 0.8967 (m-30) cc_final: 0.8170 (m-30) REVERT: A 345 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8635 (ttpt) REVERT: A 362 ASP cc_start: 0.8735 (m-30) cc_final: 0.8116 (m-30) REVERT: A 384 GLU cc_start: 0.9465 (OUTLIER) cc_final: 0.8614 (pp20) REVERT: A 393 SER cc_start: 0.9013 (m) cc_final: 0.8544 (t) REVERT: A 421 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8470 (pp20) REVERT: A 493 MET cc_start: 0.9496 (tmm) cc_final: 0.9245 (tmm) REVERT: A 570 MET cc_start: 0.9496 (mtm) cc_final: 0.9272 (mtm) REVERT: A 583 SER cc_start: 0.9513 (t) cc_final: 0.9276 (t) REVERT: A 677 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8739 (mmm160) REVERT: A 686 ARG cc_start: 0.8322 (mtp85) cc_final: 0.7980 (mtp-110) REVERT: B 53 GLU cc_start: 0.9296 (mt-10) cc_final: 0.9067 (tt0) REVERT: B 66 GLU cc_start: 0.8706 (tp30) cc_final: 0.8417 (tp30) REVERT: B 104 TYR cc_start: 0.9244 (m-80) cc_final: 0.8493 (m-80) REVERT: B 235 ARG cc_start: 0.9216 (tpp80) cc_final: 0.8895 (ttm-80) REVERT: B 274 ARG cc_start: 0.8410 (ttm-80) cc_final: 0.8026 (ttm110) REVERT: B 296 LYS cc_start: 0.8808 (mtpm) cc_final: 0.8574 (mtpp) REVERT: B 318 ASP cc_start: 0.8963 (t0) cc_final: 0.8666 (t0) REVERT: B 321 GLU cc_start: 0.8841 (tm-30) cc_final: 0.8592 (tm-30) REVERT: B 335 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8241 (mt-10) REVERT: B 348 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8662 (tmm) REVERT: B 393 SER cc_start: 0.9052 (m) cc_final: 0.8640 (t) REVERT: B 420 MET cc_start: 0.9580 (mmm) cc_final: 0.9348 (mmp) REVERT: B 483 GLU cc_start: 0.9075 (mp0) cc_final: 0.8632 (mp0) REVERT: B 603 GLU cc_start: 0.9084 (tt0) cc_final: 0.8441 (mt-10) REVERT: B 610 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8654 (ttpp) REVERT: B 612 TYR cc_start: 0.8978 (m-80) cc_final: 0.8559 (m-80) REVERT: B 624 PHE cc_start: 0.9272 (m-80) cc_final: 0.8832 (m-80) REVERT: B 686 ARG cc_start: 0.8589 (mtp-110) cc_final: 0.8102 (mtp-110) REVERT: C 68 GLU cc_start: 0.3778 (mm-30) cc_final: 0.3066 (pt0) REVERT: D 56 MET cc_start: 0.2585 (ptp) cc_final: 0.2197 (tpt) REVERT: D 74 MET cc_start: 0.2245 (OUTLIER) cc_final: 0.1933 (ptt) REVERT: D 105 TYR cc_start: -0.1231 (OUTLIER) cc_final: -0.1534 (p90) REVERT: E 34 MET cc_start: 0.6432 (mtm) cc_final: 0.6106 (pp-130) outliers start: 46 outliers final: 24 residues processed: 305 average time/residue: 0.6348 time to fit residues: 214.7316 Evaluate side-chains 306 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 274 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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 277 THR 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 409 CYS Chi-restraints excluded: chain A residue 411 LEU 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 B residue 216 VAL Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 MET 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 95 MET Chi-restraints excluded: chain C residue 97 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 0.9980 chunk 123 optimal weight: 0.6980 chunk 142 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 189 optimal weight: 50.0000 chunk 106 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** ** D 263 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 = 0.4089 r_free = 0.4089 target = 0.185845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101761 restraints weight = 23486.217| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.87 r_work: 0.2793 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2630 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 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 = 0.2636 r_free = 0.2636 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 (9 function evaluations) r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 17067 Z= 0.151 Angle : 0.605 12.817 23058 Z= 0.307 Chirality : 0.042 0.214 2468 Planarity : 0.003 0.058 2935 Dihedral : 7.885 132.829 2379 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.23 % Allowed : 21.89 % Favored : 75.88 % 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: 1176 sheet: -0.39 (0.37), residues: 173 loop : 0.25 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 235 TYR 0.022 0.001 TYR D 105 PHE 0.015 0.001 PHE A 100 TRP 0.007 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (17066) covalent geometry : angle 0.60512 / 0.31 (23056) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 1.00980 / 0.53 ( 2) hydrogen bonds : bond 0.03564 / 2.25 ( 908) hydrogen bonds : angle 4.64520 / 3.38 ( 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 330 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 290 time to evaluate : 0.679 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 40 TYR cc_start: 0.9150 (t80) cc_final: 0.8916 (t80) REVERT: A 44 ASN cc_start: 0.9445 (m-40) cc_final: 0.9037 (m-40) REVERT: A 66 GLU cc_start: 0.8656 (tp30) cc_final: 0.8288 (tp30) REVERT: A 99 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8749 (mmtm) REVERT: A 103 ASP cc_start: 0.9242 (m-30) cc_final: 0.8992 (m-30) REVERT: A 110 ASP cc_start: 0.9392 (OUTLIER) cc_final: 0.9076 (p0) REVERT: A 119 GLU cc_start: 0.9161 (mp0) cc_final: 0.8931 (mp0) REVERT: A 194 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8917 (ttmm) REVERT: A 246 SER cc_start: 0.8059 (m) cc_final: 0.7782 (p) REVERT: A 274 ARG cc_start: 0.7986 (ptp-110) cc_final: 0.7684 (ttm110) REVERT: A 286 ASP cc_start: 0.8997 (m-30) cc_final: 0.8229 (m-30) REVERT: A 345 LYS cc_start: 0.9413 (OUTLIER) cc_final: 0.8723 (ttpt) REVERT: A 362 ASP cc_start: 0.8774 (m-30) cc_final: 0.8210 (m-30) REVERT: A 384 GLU cc_start: 0.9376 (OUTLIER) cc_final: 0.8499 (pp20) REVERT: A 393 SER cc_start: 0.9095 (m) cc_final: 0.8591 (t) REVERT: A 421 GLU cc_start: 0.8778 (tm-30) cc_final: 0.8560 (pp20) REVERT: A 493 MET cc_start: 0.9548 (tmm) cc_final: 0.9312 (tmm) REVERT: A 583 SER cc_start: 0.9525 (t) cc_final: 0.9297 (t) REVERT: A 677 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8734 (mmm160) REVERT: A 686 ARG cc_start: 0.8368 (mtp85) cc_final: 0.8059 (mtp-110) REVERT: B 66 GLU cc_start: 0.8661 (tp30) cc_final: 0.8385 (tp30) REVERT: B 104 TYR cc_start: 0.9211 (m-80) cc_final: 0.8463 (m-80) REVERT: B 235 ARG cc_start: 0.9226 (tpp80) cc_final: 0.8943 (ttm-80) REVERT: B 274 ARG cc_start: 0.8477 (ttm-80) cc_final: 0.8103 (ttm110) REVERT: B 296 LYS cc_start: 0.8890 (mtpm) cc_final: 0.8672 (mtpp) REVERT: B 318 ASP cc_start: 0.8893 (t0) cc_final: 0.8590 (t0) REVERT: B 321 GLU cc_start: 0.8959 (tm-30) cc_final: 0.8639 (tm-30) REVERT: B 335 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8296 (mt-10) REVERT: B 348 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8635 (tmm) REVERT: B 393 SER cc_start: 0.9085 (m) cc_final: 0.8652 (t) REVERT: B 396 ASP cc_start: 0.8943 (m-30) cc_final: 0.8660 (m-30) REVERT: B 420 MET cc_start: 0.9578 (mmm) cc_final: 0.9325 (mmp) REVERT: B 483 GLU cc_start: 0.9108 (mp0) cc_final: 0.8687 (mp0) REVERT: B 570 MET cc_start: 0.9570 (mtm) cc_final: 0.9332 (mtm) REVERT: B 603 GLU cc_start: 0.9040 (tt0) cc_final: 0.8419 (mt-10) REVERT: B 610 LYS cc_start: 0.9061 (ttpp) cc_final: 0.8723 (ttpp) REVERT: B 612 TYR cc_start: 0.8934 (m-80) cc_final: 0.8459 (m-80) REVERT: B 624 PHE cc_start: 0.9239 (m-80) cc_final: 0.8816 (m-80) REVERT: B 686 ARG cc_start: 0.8598 (mtp-110) cc_final: 0.8280 (mtm110) REVERT: C 68 GLU cc_start: 0.3848 (mm-30) cc_final: 0.3070 (pt0) REVERT: C 103 LYS cc_start: 0.5030 (pmtt) cc_final: 0.3670 (mmmt) REVERT: D 56 MET cc_start: 0.2395 (ptp) cc_final: 0.1980 (tpt) REVERT: D 74 MET cc_start: 0.2055 (OUTLIER) cc_final: 0.1820 (ptt) REVERT: D 105 TYR cc_start: -0.1068 (OUTLIER) cc_final: -0.1412 (p90) REVERT: E 34 MET cc_start: 0.6397 (mtm) cc_final: 0.6113 (pp-130) outliers start: 40 outliers final: 23 residues processed: 312 average time/residue: 0.6160 time to fit residues: 213.2878 Evaluate side-chains 312 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 281 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 345 LYS Chi-restraints excluded: chain A residue 348 MET 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 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 B residue 216 VAL Chi-restraints excluded: chain B residue 312 GLN 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 50 ASN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 164 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 172 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.4096 r_free = 0.4096 target = 0.186110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100555 restraints weight = 23524.829| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.80 r_work: 0.2784 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2626 r_free = 0.2626 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 = 0.2626 r_free = 0.2626 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: 0.2626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17067 Z= 0.164 Angle : 0.619 13.434 23058 Z= 0.315 Chirality : 0.042 0.225 2468 Planarity : 0.003 0.057 2935 Dihedral : 7.704 133.222 2379 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.40 % Allowed : 21.78 % Favored : 75.82 % 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: 1.31 (0.19), residues: 2016 helix: 1.50 (0.15), residues: 1176 sheet: -0.41 (0.37), residues: 173 loop : 0.26 (0.23), residues: 667 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 0.014 0.001 PHE B 100 TRP 0.008 0.001 TRP D 30 HIS 0.004 0.001 HIS C 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (17066) covalent geometry : angle 0.61883 / 0.31 (23056) SS BOND : bond 0.00086 / 0.05 ( 1) SS BOND : angle 0.98606 / 0.52 ( 2) hydrogen bonds : bond 0.03597 / 2.26 ( 908) hydrogen bonds : angle 4.66470 / 3.40 ( 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 331 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 288 time to evaluate : 0.657 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 40 TYR cc_start: 0.9160 (t80) cc_final: 0.8930 (t80) REVERT: A 44 ASN cc_start: 0.9448 (m-40) cc_final: 0.9047 (m-40) REVERT: A 66 GLU cc_start: 0.8644 (tp30) cc_final: 0.8279 (tp30) REVERT: A 99 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8771 (mmtp) REVERT: A 103 ASP cc_start: 0.9259 (m-30) cc_final: 0.9023 (m-30) REVERT: A 110 ASP cc_start: 0.9395 (OUTLIER) cc_final: 0.9040 (p0) REVERT: A 194 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8851 (ttmm) REVERT: A 246 SER cc_start: 0.8089 (m) cc_final: 0.7770 (p) REVERT: A 286 ASP cc_start: 0.9000 (m-30) cc_final: 0.8238 (m-30) REVERT: A 362 ASP cc_start: 0.8755 (m-30) cc_final: 0.8190 (m-30) REVERT: A 384 GLU cc_start: 0.9365 (OUTLIER) cc_final: 0.8561 (pp20) REVERT: A 393 SER cc_start: 0.9062 (m) cc_final: 0.8622 (t) REVERT: A 421 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8490 (pp20) REVERT: A 445 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8961 (mm) REVERT: A 493 MET cc_start: 0.9533 (tmm) cc_final: 0.9280 (tmm) REVERT: A 583 SER cc_start: 0.9522 (t) cc_final: 0.9300 (t) REVERT: A 677 ARG cc_start: 0.9243 (OUTLIER) cc_final: 0.8734 (mmm160) REVERT: A 686 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8100 (mtp-110) REVERT: B 66 GLU cc_start: 0.8679 (tp30) cc_final: 0.8411 (tp30) REVERT: B 99 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8975 (mptp) REVERT: B 104 TYR cc_start: 0.9230 (m-80) cc_final: 0.8501 (m-80) REVERT: B 235 ARG cc_start: 0.9230 (tpp80) cc_final: 0.8930 (ttm-80) REVERT: B 274 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.8093 (ttm110) REVERT: B 296 LYS cc_start: 0.8903 (mtpm) cc_final: 0.8684 (mtpp) REVERT: B 318 ASP cc_start: 0.8907 (t0) cc_final: 0.8586 (t0) REVERT: B 321 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8543 (tm-30) REVERT: B 336 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9135 (ttmm) REVERT: B 348 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8665 (tmm) REVERT: B 352 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8582 (mt-10) REVERT: B 393 SER cc_start: 0.9067 (m) cc_final: 0.8616 (t) REVERT: B 483 GLU cc_start: 0.9097 (mp0) cc_final: 0.8677 (mp0) REVERT: B 570 MET cc_start: 0.9576 (mtm) cc_final: 0.9340 (mtm) REVERT: B 603 GLU cc_start: 0.9071 (tt0) cc_final: 0.8414 (mt-10) REVERT: B 610 LYS cc_start: 0.9034 (ttpp) cc_final: 0.8685 (ttpp) REVERT: B 612 TYR cc_start: 0.8926 (m-80) cc_final: 0.8450 (m-80) REVERT: B 624 PHE cc_start: 0.9265 (m-80) cc_final: 0.8822 (m-80) REVERT: B 686 ARG cc_start: 0.8578 (mtp-110) cc_final: 0.8177 (mtp-110) REVERT: C 68 GLU cc_start: 0.3702 (mm-30) cc_final: 0.2972 (pt0) REVERT: C 103 LYS cc_start: 0.4884 (pmtt) cc_final: 0.3822 (mmmt) REVERT: D 56 MET cc_start: 0.2460 (ptp) cc_final: 0.2049 (tpt) REVERT: D 74 MET cc_start: 0.2007 (OUTLIER) cc_final: 0.1716 (ptt) REVERT: D 105 TYR cc_start: -0.1101 (OUTLIER) cc_final: -0.1417 (p90) REVERT: E 34 MET cc_start: 0.6435 (mtm) cc_final: 0.6115 (pp-130) outliers start: 43 outliers final: 24 residues processed: 313 average time/residue: 0.6146 time to fit residues: 214.4268 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 : 0.475 ------------------------------------------------------------------------------- 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 348 MET 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 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 B residue 99 LYS 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 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 50 ASN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR 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 194 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 57 optimal weight: 0.6980 chunk 185 optimal weight: 50.0000 chunk 53 optimal weight: 0.9990 chunk 189 optimal weight: 40.0000 chunk 186 optimal weight: 8.9990 chunk 82 optimal weight: 0.5980 chunk 163 optimal weight: 6.9990 chunk 156 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 102 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.185493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.103076 restraints weight = 23359.166| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.85 r_work: 0.2794 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 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 = 0.2639 r_free = 0.2639 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 (9 function evaluations) r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 17067 Z= 0.165 Angle : 0.640 13.213 23058 Z= 0.323 Chirality : 0.042 0.246 2468 Planarity : 0.003 0.056 2935 Dihedral : 7.607 133.587 2379 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.29 % Allowed : 22.17 % Favored : 75.54 % 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: 1.32 (0.19), residues: 2016 helix: 1.48 (0.15), residues: 1173 sheet: -0.44 (0.37), residues: 173 loop : 0.34 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 235 TYR 0.021 0.001 TYR D 105 PHE 0.014 0.001 PHE B 100 TRP 0.007 0.001 TRP B 9 HIS 0.011 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (17066) covalent geometry : angle 0.63983 / 0.32 (23056) SS BOND : bond 0.00075 / 0.04 ( 1) SS BOND : angle 0.94629 / 0.50 ( 2) hydrogen bonds : bond 0.03603 / 2.26 ( 908) hydrogen bonds : angle 4.66408 / 3.40 ( 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: 41 poor density : 287 time to evaluate : 0.813 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 40 TYR cc_start: 0.9164 (t80) cc_final: 0.8936 (t80) REVERT: A 44 ASN cc_start: 0.9445 (m-40) cc_final: 0.9041 (m-40) REVERT: A 66 GLU cc_start: 0.8624 (tp30) cc_final: 0.8275 (tp30) REVERT: A 110 ASP cc_start: 0.9393 (OUTLIER) cc_final: 0.8750 (p0) REVERT: A 194 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8859 (ttmm) REVERT: A 246 SER cc_start: 0.8089 (m) cc_final: 0.7768 (p) REVERT: A 274 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7595 (ttm-80) REVERT: A 276 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8641 (mmmt) REVERT: A 286 ASP cc_start: 0.8976 (m-30) cc_final: 0.8208 (m-30) REVERT: A 318 ASP cc_start: 0.9029 (t0) cc_final: 0.8671 (t70) REVERT: A 362 ASP cc_start: 0.8743 (m-30) cc_final: 0.8184 (m-30) REVERT: A 384 GLU cc_start: 0.9372 (OUTLIER) cc_final: 0.8575 (pp20) REVERT: A 393 SER cc_start: 0.9108 (m) cc_final: 0.8724 (t) REVERT: A 421 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8545 (pp20) REVERT: A 445 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 493 MET cc_start: 0.9540 (tmm) cc_final: 0.9288 (tmm) REVERT: A 583 SER cc_start: 0.9540 (t) cc_final: 0.9294 (t) REVERT: A 677 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8728 (mmm160) REVERT: A 686 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8142 (mtp-110) REVERT: B 66 GLU cc_start: 0.8644 (tp30) cc_final: 0.8395 (tp30) REVERT: B 104 TYR cc_start: 0.9223 (m-80) cc_final: 0.8531 (m-80) REVERT: B 235 ARG cc_start: 0.9246 (tpp80) cc_final: 0.8936 (ttm-80) REVERT: B 274 ARG cc_start: 0.8488 (ttm-80) cc_final: 0.8111 (ttm110) REVERT: B 296 LYS cc_start: 0.8955 (mtpm) cc_final: 0.8667 (ptpp) REVERT: B 318 ASP cc_start: 0.8881 (t0) cc_final: 0.8582 (t0) REVERT: B 321 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8535 (tm-30) REVERT: B 348 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8668 (tmm) REVERT: B 352 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8545 (mt-10) REVERT: B 393 SER cc_start: 0.9073 (m) cc_final: 0.8626 (t) REVERT: B 483 GLU cc_start: 0.9104 (mp0) cc_final: 0.8736 (mp0) REVERT: B 570 MET cc_start: 0.9561 (mtm) cc_final: 0.9340 (mtm) REVERT: B 603 GLU cc_start: 0.9035 (tt0) cc_final: 0.8361 (mt-10) REVERT: B 610 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8708 (ttpp) REVERT: B 612 TYR cc_start: 0.8905 (m-80) cc_final: 0.8408 (m-80) REVERT: B 624 PHE cc_start: 0.9254 (m-80) cc_final: 0.8829 (m-80) REVERT: B 686 ARG cc_start: 0.8557 (mtp-110) cc_final: 0.8156 (mtp-110) REVERT: C 68 GLU cc_start: 0.3636 (mm-30) cc_final: 0.2902 (pt0) REVERT: C 103 LYS cc_start: 0.4883 (pmtt) cc_final: 0.3895 (mmmt) REVERT: D 56 MET cc_start: 0.2602 (ptp) cc_final: 0.2134 (tpt) REVERT: D 74 MET cc_start: 0.2144 (OUTLIER) cc_final: 0.1841 (ptt) REVERT: D 105 TYR cc_start: -0.1165 (OUTLIER) cc_final: -0.1495 (p90) REVERT: E 34 MET cc_start: 0.6445 (mtm) cc_final: 0.6133 (pp-130) outliers start: 41 outliers final: 25 residues processed: 309 average time/residue: 0.6468 time to fit residues: 221.8576 Evaluate side-chains 306 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.688 ------------------------------------------------------------------------------- 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 348 MET 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 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 B residue 216 VAL Chi-restraints excluded: chain B residue 312 GLN 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 50 ASN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS 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: 8.9990 chunk 54 optimal weight: 0.0370 chunk 179 optimal weight: 50.0000 chunk 127 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 171 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 160 optimal weight: 40.0000 chunk 64 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.189614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.106847 restraints weight = 23444.373| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.89 r_work: 0.2885 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17067 Z= 0.118 Angle : 0.616 13.135 23058 Z= 0.312 Chirality : 0.041 0.242 2468 Planarity : 0.003 0.055 2935 Dihedral : 7.279 135.063 2379 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.56 % Allowed : 22.84 % 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: 1.37 (0.19), residues: 2016 helix: 1.56 (0.15), residues: 1168 sheet: -0.20 (0.38), residues: 161 loop : 0.21 (0.23), residues: 687 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 0.014 0.001 PHE C 227 TRP 0.007 0.001 TRP B 9 HIS 0.007 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (17066) covalent geometry : angle 0.61549 / 0.31 (23056) SS BOND : bond 0.00067 / 0.04 ( 1) SS BOND : angle 0.90515 / 0.48 ( 2) hydrogen bonds : bond 0.03408 / 2.12 ( 908) hydrogen bonds : angle 4.59923 / 3.36 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9892.82 seconds wall clock time: 168 minutes 39.93 seconds (10119.93 seconds total)