Starting phenix.real_space_refine on Sun Aug 24 03:10:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byl_45037/08_2025/9byl_45037_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byl_45037/08_2025/9byl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2025/9byl_45037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2025/9byl_45037.map" model { file = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2025/9byl_45037_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byl_45037/08_2025/9byl_45037_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16706 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 4.27, per 1000 atoms: 0.26 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: 1.78 Conformation dependent library (CDL) restraints added in 771.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.58 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: 2.98 Time building geometry restraints manager: 2.23 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=" 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=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.03e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.09e+00 bond pdb=" CZ ARG B 600 " pdb=" NH2 ARG B 600 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.50e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.47e+00 ... (remaining 17061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 22314 2.10 - 4.19: 688 4.19 - 6.29: 47 6.29 - 8.38: 3 8.38 - 10.48: 4 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 - 35.68: 9886 35.68 - 71.35: 341 71.35 - 107.03: 37 107.03 - 142.71: 3 142.71 - 178.39: 3 Dihedral angle restraints: 10270 sinusoidal: 4266 harmonic: 6004 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.07 -178.39 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.03 150.65 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.04 148.93 1 2.00e+01 2.50e-03 4.46e+01 ... (remaining 10267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2230 0.094 - 0.188: 203 0.188 - 0.281: 30 0.281 - 0.375: 3 0.375 - 0.469: 2 Chirality restraints: 2468 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2465 not shown) Planarity restraints: 2935 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.077 2.00e-02 2.50e+03 3.69e-02 3.40e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 24 " 0.031 2.00e-02 2.50e+03 1.98e-02 6.83e+00 pdb=" CG PHE B 24 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 24 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE B 24 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 24 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 24 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 24 " 0.022 2.00e-02 2.50e+03 ... (remaining 2932 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 127 2.51 - 3.11: 11970 3.11 - 3.70: 28043 3.70 - 4.30: 42932 4.30 - 4.90: 67844 Nonbonded interactions: 150916 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 150911 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.100 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 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= 0.415 Angle : 0.807 13.539 23058 Z= 0.505 Chirality : 0.059 0.469 2468 Planarity : 0.004 0.041 2935 Dihedral : 17.689 178.387 6411 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 aren 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 covalent geometry : bond 0.00597 (17066) covalent geometry : angle 0.80194 (23056) SS BOND : bond 0.62925 ( 1) SS BOND : angle 9.71235 ( 2) hydrogen bonds : bond 0.15639 ( 908) hydrogen bonds : angle 6.57691 ( 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 : 0.678 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: 0.6532 time to fit residues: 355.7363 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 : 0.640 ------------------------------------------------------------------------------- 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: 5.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 410 ASN A 668 ASN B 150 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 84 HIS C 119 ASN C 238 ASN D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.186305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097642 restraints weight = 22647.999| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 2.74 r_work: 0.2756 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 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 = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2383 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= 0.223 Angle : 0.630 12.711 23058 Z= 0.328 Chirality : 0.044 0.207 2468 Planarity : 0.004 0.042 2935 Dihedral : 11.358 179.137 2345 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 17.81 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.67 (0.18), residues: 2016 helix: 1.59 (0.15), residues: 1165 sheet: 0.51 (0.40), residues: 153 loop : 0.61 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.020 0.001 TYR C 213 PHE 0.017 0.001 PHE B 100 TRP 0.009 0.001 TRP B 9 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00502 (17066) covalent geometry : angle 0.63021 (23056) SS BOND : bond 0.01284 ( 1) SS BOND : angle 1.86918 ( 2) hydrogen bonds : bond 0.04776 ( 908) hydrogen bonds : angle 5.00444 ( 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: 70 poor density : 307 time to evaluate : 0.633 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: 0.9231 (m-30) cc_final: 0.8965 (m-30) REVERT: A 66 GLU cc_start: 0.8702 (tp30) cc_final: 0.8398 (tp30) REVERT: A 67 GLU cc_start: 0.8949 (mp0) cc_final: 0.8692 (mp0) REVERT: A 99 LYS cc_start: 0.8928 (mmtt) cc_final: 0.8714 (mmtp) REVERT: A 103 ASP cc_start: 0.9210 (m-30) cc_final: 0.8837 (m-30) REVERT: A 110 ASP cc_start: 0.9343 (OUTLIER) cc_final: 0.8555 (p0) REVERT: A 184 ARG cc_start: 0.8850 (ttm-80) cc_final: 0.8636 (ttm-80) REVERT: A 246 SER cc_start: 0.8121 (m) cc_final: 0.7731 (p) REVERT: A 270 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7879 (OUTLIER) REVERT: A 274 ARG cc_start: 0.8299 (ptp-110) cc_final: 0.8040 (ptp-110) REVERT: A 286 ASP cc_start: 0.8934 (m-30) cc_final: 0.8377 (m-30) REVERT: A 362 ASP cc_start: 0.8685 (m-30) cc_final: 0.8294 (m-30) REVERT: A 384 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.8594 (pp20) REVERT: A 421 GLU cc_start: 0.8698 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 583 SER cc_start: 0.9341 (t) cc_final: 0.9133 (t) REVERT: A 686 ARG cc_start: 0.8261 (mtp85) cc_final: 0.7946 (mtp85) REVERT: B 112 LYS cc_start: 0.9300 (mtmm) cc_final: 0.9067 (mtmm) REVERT: B 139 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8934 (mt-10) REVERT: B 274 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7849 (ttm110) REVERT: B 321 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 483 GLU cc_start: 0.9059 (mp0) cc_final: 0.8603 (mp0) REVERT: B 603 GLU cc_start: 0.9082 (tt0) cc_final: 0.8316 (mt-10) REVERT: B 612 TYR cc_start: 0.9090 (m-80) cc_final: 0.8563 (m-80) REVERT: B 624 PHE cc_start: 0.9170 (m-80) cc_final: 0.8740 (m-80) REVERT: C 96 MET cc_start: 0.7985 (mmm) cc_final: 0.7681 (mmt) REVERT: C 137 MET cc_start: 0.1124 (mtp) cc_final: 0.0797 (mmp) REVERT: D 56 MET cc_start: 0.2141 (ptp) cc_final: 0.1830 (tpt) REVERT: D 146 GLN cc_start: 0.6441 (OUTLIER) cc_final: 0.6117 (mp10) REVERT: D 235 LEU cc_start: 0.7681 (mt) cc_final: 0.7475 (pp) outliers start: 70 outliers final: 23 residues processed: 352 average time/residue: 0.5700 time to fit residues: 222.6486 Evaluate side-chains 304 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 278 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 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 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 146 GLN Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 80 optimal weight: 0.9980 chunk 167 optimal weight: 40.0000 chunk 189 optimal weight: 40.0000 chunk 193 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 668 ASN B 180 ASN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 128 ASN D 132 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN D 238 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.189887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102421 restraints weight = 23070.275| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.91 r_work: 0.2801 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 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 = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2895 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= 0.136 Angle : 0.576 10.594 23058 Z= 0.295 Chirality : 0.041 0.170 2468 Planarity : 0.003 0.042 2935 Dihedral : 10.929 178.184 2337 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.18 % Allowed : 17.81 % Favored : 79.01 % 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 aren not related in a simple way. whole: 1.57 (0.18), residues: 2016 helix: 1.61 (0.15), residues: 1174 sheet: 0.29 (0.40), residues: 153 loop : 0.39 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.022 0.001 TYR D 105 PHE 0.016 0.001 PHE A 100 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00296 (17066) covalent geometry : angle 0.57586 (23056) SS BOND : bond 0.00204 ( 1) SS BOND : angle 1.60440 ( 2) hydrogen bonds : bond 0.04015 ( 908) hydrogen bonds : angle 4.71239 ( 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: 57 poor density : 312 time to evaluate : 0.635 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: 0.9207 (m-30) cc_final: 0.8994 (m-30) REVERT: A 66 GLU cc_start: 0.8701 (tp30) cc_final: 0.8403 (tp30) REVERT: A 99 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8832 (mmtp) REVERT: A 103 ASP cc_start: 0.9210 (m-30) cc_final: 0.8903 (m-30) REVERT: A 110 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.9105 (p0) REVERT: A 246 SER cc_start: 0.8206 (m) cc_final: 0.7891 (p) REVERT: A 270 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7972 (OUTLIER) REVERT: A 286 ASP cc_start: 0.8979 (m-30) cc_final: 0.8478 (m-30) REVERT: A 317 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9100 (mtp) REVERT: A 345 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.8751 (ttpt) REVERT: A 362 ASP cc_start: 0.8744 (m-30) cc_final: 0.8388 (m-30) REVERT: A 384 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.8664 (pp20) REVERT: A 393 SER cc_start: 0.9079 (m) cc_final: 0.8622 (t) REVERT: A 493 MET cc_start: 0.9563 (tmm) cc_final: 0.9348 (tmm) REVERT: A 583 SER cc_start: 0.9512 (OUTLIER) cc_final: 0.9291 (t) REVERT: A 686 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8000 (mtp85) REVERT: B 23 LYS cc_start: 0.9023 (mtmm) cc_final: 0.8721 (mtmt) REVERT: B 139 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9018 (mt-10) REVERT: B 231 ASP cc_start: 0.9161 (t0) cc_final: 0.8959 (t0) REVERT: B 232 ASN cc_start: 0.9122 (m110) cc_final: 0.8912 (m-40) REVERT: B 235 ARG cc_start: 0.9141 (ttm-80) cc_final: 0.8717 (ttm-80) REVERT: B 274 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.7966 (ttm110) REVERT: B 321 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8593 (tm-30) REVERT: B 335 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8246 (mt-10) REVERT: B 384 GLU cc_start: 0.9392 (OUTLIER) cc_final: 0.8965 (pp20) REVERT: B 393 SER cc_start: 0.9186 (m) cc_final: 0.8822 (t) REVERT: B 446 ARG cc_start: 0.8186 (mmm-85) cc_final: 0.7960 (mmm-85) REVERT: B 483 GLU cc_start: 0.9115 (mp0) cc_final: 0.8735 (mp0) REVERT: B 603 GLU cc_start: 0.9032 (tt0) cc_final: 0.8517 (mt-10) REVERT: B 612 TYR cc_start: 0.9000 (m-80) cc_final: 0.8608 (m-80) REVERT: B 624 PHE cc_start: 0.9149 (m-80) cc_final: 0.8783 (m-80) REVERT: B 686 ARG cc_start: 0.8626 (mtp-110) cc_final: 0.8158 (mtp-110) REVERT: C 85 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6594 (tm-30) REVERT: C 96 MET cc_start: 0.7799 (mmm) cc_final: 0.7488 (mmt) REVERT: C 123 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7988 (tp30) REVERT: C 204 TYR cc_start: 0.5612 (OUTLIER) cc_final: 0.5193 (p90) REVERT: D 56 MET cc_start: 0.2238 (ptp) cc_final: 0.1783 (tpt) REVERT: D 105 TYR cc_start: -0.1498 (OUTLIER) cc_final: -0.1827 (p90) REVERT: D 190 ILE cc_start: 0.3807 (OUTLIER) cc_final: 0.3606 (mt) outliers start: 57 outliers final: 19 residues processed: 345 average time/residue: 0.5453 time to fit residues: 209.5457 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 : 0.649 ------------------------------------------------------------------------------- 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 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 583 SER 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 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 105 TYR Chi-restraints excluded: chain D residue 190 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 109 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 239 GLN A 668 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.186479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.099804 restraints weight = 22712.647| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.69 r_work: 0.2780 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2627 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2627 r_free = 0.2627 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2627 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17067 Z= 0.163 Angle : 0.586 11.611 23058 Z= 0.298 Chirality : 0.042 0.209 2468 Planarity : 0.003 0.045 2935 Dihedral : 10.709 177.699 2335 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.41 % Allowed : 19.60 % Favored : 77.00 % 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 aren not related in a simple way. whole: 1.55 (0.18), residues: 2016 helix: 1.62 (0.15), residues: 1174 sheet: 0.25 (0.40), residues: 153 loop : 0.34 (0.23), residues: 689 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 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00365 (17066) covalent geometry : angle 0.58548 (23056) SS BOND : bond 0.00159 ( 1) SS BOND : angle 1.32858 ( 2) hydrogen bonds : bond 0.03763 ( 908) hydrogen bonds : angle 4.63882 ( 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 356 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 0.687 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: A 39 ASP cc_start: 0.9205 (m-30) cc_final: 0.8991 (m-30) REVERT: A 66 GLU cc_start: 0.8699 (tp30) cc_final: 0.8354 (tp30) REVERT: A 99 LYS cc_start: 0.9105 (mmtt) cc_final: 0.8846 (mmtp) REVERT: A 103 ASP cc_start: 0.9221 (m-30) cc_final: 0.8973 (m-30) REVERT: A 110 ASP cc_start: 0.9312 (OUTLIER) cc_final: 0.9076 (p0) REVERT: A 246 SER cc_start: 0.8258 (m) cc_final: 0.7915 (p) REVERT: A 345 LYS cc_start: 0.9445 (OUTLIER) cc_final: 0.8753 (ttpt) REVERT: A 362 ASP cc_start: 0.8767 (m-30) cc_final: 0.8514 (m-30) REVERT: A 384 GLU cc_start: 0.9414 (OUTLIER) cc_final: 0.8619 (pp20) REVERT: A 393 SER cc_start: 0.9071 (m) cc_final: 0.8605 (t) REVERT: A 394 TYR cc_start: 0.9326 (m-80) cc_final: 0.9112 (m-80) REVERT: A 421 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8439 (pp20) REVERT: A 445 ILE cc_start: 0.9251 (mm) cc_final: 0.8698 (mm) REVERT: A 446 ARG cc_start: 0.7417 (mmp-170) cc_final: 0.6939 (mmp-170) REVERT: A 493 MET cc_start: 0.9566 (tmm) cc_final: 0.9352 (tmm) REVERT: A 583 SER cc_start: 0.9515 (OUTLIER) cc_final: 0.9284 (t) REVERT: A 598 MET cc_start: 0.9373 (mtm) cc_final: 0.9122 (mtm) REVERT: B 66 GLU cc_start: 0.8727 (tp30) cc_final: 0.8518 (tp30) REVERT: B 274 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.7981 (ttm110) REVERT: B 318 ASP cc_start: 0.8762 (t0) cc_final: 0.8506 (t0) REVERT: B 321 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8638 (tm-30) REVERT: B 335 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8213 (mt-10) REVERT: B 348 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8538 (tmm) REVERT: B 384 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8887 (pp20) REVERT: B 393 SER cc_start: 0.9165 (m) cc_final: 0.8815 (t) REVERT: B 446 ARG cc_start: 0.8349 (mmm-85) cc_final: 0.8083 (mmm-85) REVERT: B 483 GLU cc_start: 0.9126 (mp0) cc_final: 0.8722 (mp0) REVERT: B 603 GLU cc_start: 0.9050 (tt0) cc_final: 0.8525 (mt-10) REVERT: B 612 TYR cc_start: 0.8994 (m-80) cc_final: 0.8596 (m-80) REVERT: B 624 PHE cc_start: 0.9188 (m-80) cc_final: 0.8800 (m-80) REVERT: B 686 ARG cc_start: 0.8664 (mtp-110) cc_final: 0.8211 (mtp-110) REVERT: C 85 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: C 93 MET cc_start: 0.7732 (mtt) cc_final: 0.7432 (ttt) REVERT: C 95 MET cc_start: 0.2026 (OUTLIER) cc_final: 0.1824 (ptt) REVERT: C 147 LYS cc_start: 0.2803 (mmtm) cc_final: 0.2441 (mppt) REVERT: D 105 TYR cc_start: -0.1370 (OUTLIER) cc_final: -0.1708 (p90) REVERT: D 110 MET cc_start: 0.8228 (pp-130) cc_final: 0.7624 (mmm) outliers start: 61 outliers final: 25 residues processed: 326 average time/residue: 0.5696 time to fit residues: 206.0564 Evaluate side-chains 311 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 277 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 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 231 ASP 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 C residue 85 GLN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET 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: 10.0000 chunk 52 optimal weight: 1.9990 chunk 163 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 194 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN 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** B 410 ASN C 127 GLN D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.184377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.096455 restraints weight = 22899.180| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.78 r_work: 0.2692 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 17067 Z= 0.324 Angle : 0.639 11.246 23058 Z= 0.327 Chirality : 0.045 0.183 2468 Planarity : 0.003 0.048 2935 Dihedral : 10.934 177.716 2335 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.57 % Allowed : 19.65 % Favored : 76.77 % 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 aren not related in a simple way. whole: 1.42 (0.18), residues: 2016 helix: 1.52 (0.15), residues: 1181 sheet: 0.17 (0.39), residues: 157 loop : 0.27 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 164 TYR 0.023 0.002 TYR D 174 PHE 0.017 0.002 PHE B 492 TRP 0.010 0.001 TRP A 623 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00733 (17066) covalent geometry : angle 0.63929 (23056) SS BOND : bond 0.00176 ( 1) SS BOND : angle 1.25129 ( 2) hydrogen bonds : bond 0.03952 ( 908) hydrogen bonds : angle 4.73990 ( 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 340 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 276 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8751 (tp30) cc_final: 0.8378 (tp30) REVERT: A 110 ASP cc_start: 0.9338 (OUTLIER) cc_final: 0.9124 (p0) REVERT: A 246 SER cc_start: 0.8213 (m) cc_final: 0.7859 (p) REVERT: A 286 ASP cc_start: 0.8998 (m-30) cc_final: 0.8532 (m-30) REVERT: A 345 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8703 (ttpt) REVERT: A 362 ASP cc_start: 0.8850 (m-30) cc_final: 0.8501 (m-30) REVERT: A 384 GLU cc_start: 0.9501 (OUTLIER) cc_final: 0.9148 (pp20) REVERT: A 393 SER cc_start: 0.9133 (m) cc_final: 0.8670 (t) REVERT: A 445 ILE cc_start: 0.9456 (mm) cc_final: 0.9144 (mm) REVERT: A 446 ARG cc_start: 0.7611 (mmp-170) cc_final: 0.7391 (mmp-170) REVERT: A 570 MET cc_start: 0.9482 (mtm) cc_final: 0.9246 (mtm) REVERT: A 583 SER cc_start: 0.9575 (t) cc_final: 0.9316 (t) REVERT: A 677 ARG cc_start: 0.9252 (OUTLIER) cc_final: 0.8777 (mmm160) REVERT: A 686 ARG cc_start: 0.8415 (mtp85) cc_final: 0.8158 (mtp-110) REVERT: B 66 GLU cc_start: 0.8831 (tp30) cc_final: 0.8572 (tp30) REVERT: B 217 GLU cc_start: 0.9003 (mp0) cc_final: 0.8769 (mm-30) REVERT: B 274 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8056 (ttm110) REVERT: B 318 ASP cc_start: 0.8872 (t0) cc_final: 0.8580 (t0) REVERT: B 321 GLU cc_start: 0.8910 (tm-30) cc_final: 0.8555 (tm-30) REVERT: B 335 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8275 (mt-10) REVERT: B 336 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.8991 (ttmm) REVERT: B 348 MET cc_start: 0.9068 (OUTLIER) cc_final: 0.8664 (tmm) REVERT: B 384 GLU cc_start: 0.9449 (OUTLIER) cc_final: 0.8902 (pp20) REVERT: B 393 SER cc_start: 0.9173 (m) cc_final: 0.8810 (t) REVERT: B 483 GLU cc_start: 0.9158 (mp0) cc_final: 0.8776 (mp0) REVERT: B 603 GLU cc_start: 0.9085 (tt0) cc_final: 0.8439 (mt-10) REVERT: B 610 LYS cc_start: 0.8950 (ttpp) cc_final: 0.8626 (ttmm) REVERT: B 612 TYR cc_start: 0.9137 (m-80) cc_final: 0.8639 (m-80) REVERT: B 624 PHE cc_start: 0.9321 (m-80) cc_final: 0.8898 (m-80) REVERT: B 686 ARG cc_start: 0.8736 (mtp-110) cc_final: 0.8289 (mtp-110) REVERT: C 85 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6346 (tm-30) REVERT: C 147 LYS cc_start: 0.2610 (mmtm) cc_final: 0.2403 (mppt) REVERT: C 269 MET cc_start: 0.4460 (mpt) cc_final: 0.4134 (ptp) REVERT: D 56 MET cc_start: 0.2652 (ptp) cc_final: 0.2258 (tpt) REVERT: D 105 TYR cc_start: -0.1275 (OUTLIER) cc_final: -0.1574 (p90) REVERT: E 34 MET cc_start: 0.6421 (mtm) cc_final: 0.6120 (pp-130) outliers start: 64 outliers final: 30 residues processed: 315 average time/residue: 0.5776 time to fit residues: 201.0036 Evaluate side-chains 301 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 262 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 178 SER 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 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 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 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 546 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET 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: 0.7980 chunk 22 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 170 optimal weight: 50.0000 chunk 116 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 668 ASN C 25 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.188338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.101672 restraints weight = 22807.907| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.81 r_work: 0.2776 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 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 = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3520 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= 0.142 Angle : 0.592 11.434 23058 Z= 0.300 Chirality : 0.041 0.204 2468 Planarity : 0.003 0.054 2935 Dihedral : 10.613 175.909 2335 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.90 % Allowed : 20.99 % Favored : 76.10 % 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 aren not related in a simple way. whole: 1.43 (0.18), residues: 2016 helix: 1.56 (0.15), residues: 1179 sheet: 0.09 (0.39), residues: 157 loop : 0.23 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 235 TYR 0.029 0.001 TYR D 174 PHE 0.017 0.001 PHE A 100 TRP 0.007 0.001 TRP B 9 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00318 (17066) covalent geometry : angle 0.59199 (23056) SS BOND : bond 0.00111 ( 1) SS BOND : angle 1.11335 ( 2) hydrogen bonds : bond 0.03597 ( 908) hydrogen bonds : angle 4.62316 ( 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 353 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.494 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: 0.9200 (t80) cc_final: 0.8973 (t80) REVERT: A 44 ASN cc_start: 0.9443 (m-40) cc_final: 0.9033 (m-40) REVERT: A 66 GLU cc_start: 0.8682 (tp30) cc_final: 0.8294 (tp30) REVERT: A 99 LYS cc_start: 0.9177 (mmtp) cc_final: 0.8827 (mmtt) REVERT: A 103 ASP cc_start: 0.9215 (m-30) cc_final: 0.8943 (m-30) REVERT: A 246 SER cc_start: 0.8122 (m) cc_final: 0.7827 (p) REVERT: A 274 ARG cc_start: 0.8317 (ptp-110) cc_final: 0.7909 (ttm110) REVERT: A 286 ASP cc_start: 0.8981 (m-30) cc_final: 0.8223 (m-30) REVERT: A 345 LYS cc_start: 0.9460 (OUTLIER) cc_final: 0.8751 (ttpt) REVERT: A 362 ASP cc_start: 0.8742 (m-30) cc_final: 0.8182 (m-30) REVERT: A 384 GLU cc_start: 0.9444 (OUTLIER) cc_final: 0.8719 (pp20) REVERT: A 393 SER cc_start: 0.9140 (m) cc_final: 0.8721 (t) REVERT: A 421 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8501 (pp20) REVERT: A 445 ILE cc_start: 0.9424 (mm) cc_final: 0.9049 (mm) REVERT: A 446 ARG cc_start: 0.7576 (mmp-170) cc_final: 0.7317 (mmp-170) REVERT: A 570 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.9193 (mtm) REVERT: A 583 SER cc_start: 0.9577 (t) cc_final: 0.9300 (t) REVERT: A 598 MET cc_start: 0.9395 (mtm) cc_final: 0.8882 (mtm) REVERT: A 677 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8702 (mmm160) REVERT: A 686 ARG cc_start: 0.8489 (mtp85) cc_final: 0.7995 (mtp85) REVERT: B 53 GLU cc_start: 0.9306 (mt-10) cc_final: 0.9094 (tt0) REVERT: B 66 GLU cc_start: 0.8779 (tp30) cc_final: 0.8520 (tp30) REVERT: B 221 LYS cc_start: 0.9379 (mttm) cc_final: 0.9158 (mttp) REVERT: B 274 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8167 (ttm110) REVERT: B 296 LYS cc_start: 0.8910 (mtpm) cc_final: 0.8694 (mtpp) REVERT: B 318 ASP cc_start: 0.8923 (t0) cc_final: 0.8627 (t0) REVERT: B 321 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8603 (tm-30) REVERT: B 348 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8675 (tmm) REVERT: B 393 SER cc_start: 0.9151 (m) cc_final: 0.8768 (t) REVERT: B 483 GLU cc_start: 0.9112 (mp0) cc_final: 0.8741 (mp0) REVERT: B 603 GLU cc_start: 0.9031 (tt0) cc_final: 0.8475 (mt-10) REVERT: B 610 LYS cc_start: 0.9021 (ttpp) cc_final: 0.8695 (ttmm) REVERT: B 612 TYR cc_start: 0.9012 (m-80) cc_final: 0.8606 (m-80) REVERT: B 624 PHE cc_start: 0.9224 (m-80) cc_final: 0.8803 (m-80) REVERT: B 686 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8299 (mtp-110) REVERT: C 85 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6376 (tm-30) REVERT: C 269 MET cc_start: 0.4090 (mpt) cc_final: 0.3876 (ptp) REVERT: D 56 MET cc_start: 0.2596 (ptp) cc_final: 0.2190 (tpt) REVERT: D 105 TYR cc_start: -0.1204 (OUTLIER) cc_final: -0.1502 (p90) REVERT: E 34 MET cc_start: 0.6384 (mtm) cc_final: 0.6141 (pp-130) outliers start: 52 outliers final: 23 residues processed: 328 average time/residue: 0.5552 time to fit residues: 202.5223 Evaluate side-chains 301 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 345 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 50 ASN 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 D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 157 MET 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: 8.9990 chunk 12 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 183 optimal weight: 40.0000 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 143 optimal weight: 40.0000 chunk 80 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 191 GLN B 218 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 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 = 0.4069 r_free = 0.4069 target = 0.185736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.100464 restraints weight = 22940.781| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.73 r_work: 0.2745 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2590 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 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 = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17067 Z= 0.204 Angle : 0.615 12.026 23058 Z= 0.311 Chirality : 0.043 0.211 2468 Planarity : 0.003 0.057 2935 Dihedral : 10.487 177.210 2333 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.90 % Allowed : 21.33 % Favored : 75.77 % 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 aren not related in a simple way. whole: 1.39 (0.18), residues: 2016 helix: 1.52 (0.15), residues: 1180 sheet: 0.04 (0.39), residues: 157 loop : 0.23 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.022 0.001 TYR D 105 PHE 0.016 0.001 PHE B 100 TRP 0.009 0.001 TRP D 30 HIS 0.004 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00464 (17066) covalent geometry : angle 0.61452 (23056) SS BOND : bond 0.00123 ( 1) SS BOND : angle 1.07760 ( 2) hydrogen bonds : bond 0.03629 ( 908) hydrogen bonds : angle 4.64685 ( 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 332 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9165 (t80) cc_final: 0.8873 (t80) REVERT: A 44 ASN cc_start: 0.9410 (m-40) cc_final: 0.8970 (m-40) REVERT: A 66 GLU cc_start: 0.8647 (tp30) cc_final: 0.8260 (tp30) REVERT: A 99 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8816 (mmtt) REVERT: A 246 SER cc_start: 0.7975 (m) cc_final: 0.7638 (p) REVERT: A 274 ARG cc_start: 0.7944 (ptp-110) cc_final: 0.7551 (ttm-80) REVERT: A 318 ASP cc_start: 0.9035 (t0) cc_final: 0.8690 (t70) REVERT: A 345 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8627 (ttpt) REVERT: A 362 ASP cc_start: 0.8743 (m-30) cc_final: 0.8460 (m-30) REVERT: A 384 GLU cc_start: 0.9458 (OUTLIER) cc_final: 0.9092 (pp20) REVERT: A 393 SER cc_start: 0.9016 (m) cc_final: 0.8547 (t) REVERT: A 421 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8445 (pp20) REVERT: A 446 ARG cc_start: 0.7586 (mmp-170) cc_final: 0.7301 (mmp-170) REVERT: A 570 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.9273 (mtm) REVERT: A 583 SER cc_start: 0.9544 (t) cc_final: 0.9235 (t) REVERT: A 598 MET cc_start: 0.9389 (mtm) cc_final: 0.8812 (mtm) REVERT: A 677 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8788 (mmm160) REVERT: A 686 ARG cc_start: 0.8402 (mtp85) cc_final: 0.7843 (mtp85) REVERT: B 53 GLU cc_start: 0.9285 (mt-10) cc_final: 0.9075 (tt0) REVERT: B 66 GLU cc_start: 0.8749 (tp30) cc_final: 0.8449 (tp30) REVERT: B 274 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8009 (ttm110) REVERT: B 296 LYS cc_start: 0.8813 (mtpm) cc_final: 0.8574 (mtpp) REVERT: B 318 ASP cc_start: 0.8944 (t0) cc_final: 0.8646 (t0) REVERT: B 321 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 336 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.9001 (ttmm) REVERT: B 348 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: B 393 SER cc_start: 0.9101 (m) cc_final: 0.8678 (t) REVERT: B 406 ASP cc_start: 0.8857 (m-30) cc_final: 0.8642 (m-30) REVERT: B 483 GLU cc_start: 0.9073 (mp0) cc_final: 0.8623 (mp0) REVERT: B 603 GLU cc_start: 0.9077 (tt0) cc_final: 0.8544 (mt-10) REVERT: B 610 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8640 (ttmm) REVERT: B 612 TYR cc_start: 0.9030 (m-80) cc_final: 0.8565 (m-80) REVERT: B 624 PHE cc_start: 0.9277 (m-80) cc_final: 0.8812 (m-80) REVERT: B 686 ARG cc_start: 0.8615 (mtp-110) cc_final: 0.8113 (mtp-110) REVERT: C 269 MET cc_start: 0.4322 (OUTLIER) cc_final: 0.4110 (ptp) REVERT: D 56 MET cc_start: 0.2504 (ptp) cc_final: 0.2096 (tpt) REVERT: D 105 TYR cc_start: -0.1058 (OUTLIER) cc_final: -0.1353 (p90) REVERT: E 34 MET cc_start: 0.6416 (mtm) cc_final: 0.6118 (pp-130) outliers start: 52 outliers final: 28 residues processed: 307 average time/residue: 0.5418 time to fit residues: 184.5193 Evaluate side-chains 300 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 264 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 345 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 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 B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP 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 269 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 103 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 7 optimal weight: 0.9990 chunk 123 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 189 optimal weight: 50.0000 chunk 106 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 144 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 668 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.186844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.104861 restraints weight = 23199.111| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.84 r_work: 0.2802 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 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 = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 17067 Z= 0.143 Angle : 0.612 12.525 23058 Z= 0.307 Chirality : 0.042 0.209 2468 Planarity : 0.003 0.058 2935 Dihedral : 10.127 177.059 2331 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.46 % Allowed : 21.83 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.19), residues: 2016 helix: 1.52 (0.15), residues: 1174 sheet: -0.32 (0.37), residues: 177 loop : 0.26 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.021 0.001 TYR D 105 PHE 0.015 0.001 PHE B 100 TRP 0.007 0.001 TRP D 30 HIS 0.004 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00325 (17066) covalent geometry : angle 0.61175 (23056) SS BOND : bond 0.00091 ( 1) SS BOND : angle 0.99531 ( 2) hydrogen bonds : bond 0.03514 ( 908) hydrogen bonds : angle 4.65155 ( 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 344 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 0.627 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 40 TYR cc_start: 0.9212 (t80) cc_final: 0.8937 (t80) REVERT: A 44 ASN cc_start: 0.9451 (m-40) cc_final: 0.9037 (m-40) REVERT: A 66 GLU cc_start: 0.8632 (tp30) cc_final: 0.8273 (tp30) REVERT: A 99 LYS cc_start: 0.9116 (mmtp) cc_final: 0.8681 (mmtt) REVERT: A 103 ASP cc_start: 0.9216 (m-30) cc_final: 0.8937 (m-30) REVERT: A 110 ASP cc_start: 0.9346 (OUTLIER) cc_final: 0.8738 (p0) REVERT: A 246 SER cc_start: 0.8060 (m) cc_final: 0.7782 (p) REVERT: A 274 ARG cc_start: 0.7829 (ptp-110) cc_final: 0.7421 (ttm-80) REVERT: A 286 ASP cc_start: 0.9001 (m-30) cc_final: 0.8217 (m-30) REVERT: A 362 ASP cc_start: 0.8804 (m-30) cc_final: 0.8216 (m-30) REVERT: A 384 GLU cc_start: 0.9444 (OUTLIER) cc_final: 0.9121 (pp20) REVERT: A 393 SER cc_start: 0.9077 (m) cc_final: 0.8613 (t) REVERT: A 421 GLU cc_start: 0.8774 (tm-30) cc_final: 0.8551 (pp20) REVERT: A 445 ILE cc_start: 0.9307 (mm) cc_final: 0.8863 (mm) REVERT: A 446 ARG cc_start: 0.7554 (mmp-170) cc_final: 0.7240 (mmp-170) REVERT: A 570 MET cc_start: 0.9465 (OUTLIER) cc_final: 0.9221 (mtm) REVERT: A 583 SER cc_start: 0.9548 (t) cc_final: 0.9279 (t) REVERT: A 677 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8729 (mmm160) REVERT: A 686 ARG cc_start: 0.8491 (mtp85) cc_final: 0.8147 (mtp85) REVERT: B 66 GLU cc_start: 0.8702 (tp30) cc_final: 0.8419 (tp30) REVERT: B 184 ARG cc_start: 0.9292 (tpp-160) cc_final: 0.8768 (tpp80) REVERT: B 235 ARG cc_start: 0.9033 (ttm-80) cc_final: 0.8759 (ttm-80) REVERT: B 274 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8170 (ttm110) REVERT: B 296 LYS cc_start: 0.8906 (mtpm) cc_final: 0.8693 (mtpp) REVERT: B 318 ASP cc_start: 0.8893 (t0) cc_final: 0.8605 (t0) REVERT: B 321 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8530 (tm-30) REVERT: B 348 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8664 (tmm) REVERT: B 393 SER cc_start: 0.9103 (m) cc_final: 0.8656 (t) REVERT: B 483 GLU cc_start: 0.9114 (mp0) cc_final: 0.8702 (mp0) REVERT: B 603 GLU cc_start: 0.9015 (tt0) cc_final: 0.8423 (mt-10) REVERT: B 610 LYS cc_start: 0.9058 (ttpp) cc_final: 0.8728 (ttpp) REVERT: B 612 TYR cc_start: 0.8970 (m-80) cc_final: 0.8462 (m-80) REVERT: B 624 PHE cc_start: 0.9267 (m-80) cc_final: 0.8817 (m-80) REVERT: B 686 ARG cc_start: 0.8634 (mtp-110) cc_final: 0.8288 (mtm110) REVERT: D 105 TYR cc_start: -0.1092 (OUTLIER) cc_final: -0.1379 (p90) REVERT: E 34 MET cc_start: 0.6412 (mtm) cc_final: 0.6102 (pp-130) outliers start: 44 outliers final: 22 residues processed: 325 average time/residue: 0.5422 time to fit residues: 195.7726 Evaluate side-chains 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 570 MET Chi-restraints excluded: chain A residue 587 VAL 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 348 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR 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 103 LYS 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: 7.9990 chunk 198 optimal weight: 10.0000 chunk 5 optimal weight: 0.0980 chunk 25 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 172 optimal weight: 50.0000 chunk 77 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 71 optimal weight: 0.0170 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** 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 = 0.4123 r_free = 0.4123 target = 0.189087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.104005 restraints weight = 23467.675| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.96 r_work: 0.2844 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 17067 Z= 0.125 Angle : 0.620 13.379 23058 Z= 0.312 Chirality : 0.042 0.245 2468 Planarity : 0.003 0.057 2935 Dihedral : 9.850 176.306 2331 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.79 % Allowed : 22.67 % 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 aren not related in a simple way. whole: 1.33 (0.19), residues: 2016 helix: 1.53 (0.15), residues: 1169 sheet: -0.36 (0.37), residues: 177 loop : 0.25 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 235 TYR 0.021 0.001 TYR D 105 PHE 0.014 0.001 PHE A 100 TRP 0.007 0.001 TRP B 9 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00281 (17066) covalent geometry : angle 0.61946 (23056) SS BOND : bond 0.00081 ( 1) SS BOND : angle 0.96966 ( 2) hydrogen bonds : bond 0.03471 ( 908) hydrogen bonds : angle 4.65961 ( 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 338 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 0.470 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: 0.9134 (t80) cc_final: 0.8858 (t80) REVERT: A 44 ASN cc_start: 0.9393 (m-40) cc_final: 0.8971 (m-40) REVERT: A 66 GLU cc_start: 0.8379 (tp30) cc_final: 0.8041 (tp30) REVERT: A 99 LYS cc_start: 0.8974 (mmtp) cc_final: 0.8512 (mmtt) REVERT: A 110 ASP cc_start: 0.9259 (OUTLIER) cc_final: 0.8625 (p0) REVERT: A 231 ASP cc_start: 0.8791 (t0) cc_final: 0.8490 (t70) REVERT: A 246 SER cc_start: 0.7932 (m) cc_final: 0.7702 (p) REVERT: A 274 ARG cc_start: 0.7777 (ptp-110) cc_final: 0.7369 (ttm-80) REVERT: A 286 ASP cc_start: 0.8842 (m-30) cc_final: 0.8028 (m-30) REVERT: A 318 ASP cc_start: 0.8905 (t0) cc_final: 0.8567 (t70) REVERT: A 362 ASP cc_start: 0.8512 (m-30) cc_final: 0.7897 (m-30) REVERT: A 384 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8909 (pp20) REVERT: A 393 SER cc_start: 0.8972 (m) cc_final: 0.8557 (t) REVERT: A 421 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8331 (pp20) REVERT: A 445 ILE cc_start: 0.9249 (mm) cc_final: 0.8831 (mm) REVERT: A 446 ARG cc_start: 0.7500 (mmp-170) cc_final: 0.7217 (mmp-170) REVERT: A 570 MET cc_start: 0.9295 (OUTLIER) cc_final: 0.9075 (mtm) REVERT: A 583 SER cc_start: 0.9486 (t) cc_final: 0.9184 (t) REVERT: A 686 ARG cc_start: 0.8334 (mtp85) cc_final: 0.8043 (mtp-110) REVERT: B 66 GLU cc_start: 0.8426 (tp30) cc_final: 0.8186 (tp30) REVERT: B 99 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8876 (mptp) REVERT: B 184 ARG cc_start: 0.9207 (tpp-160) cc_final: 0.8678 (tpp80) REVERT: B 235 ARG cc_start: 0.8879 (ttm-80) cc_final: 0.8620 (ttm-80) REVERT: B 296 LYS cc_start: 0.8922 (mtpm) cc_final: 0.8682 (ptpp) REVERT: B 318 ASP cc_start: 0.8804 (t0) cc_final: 0.8541 (t0) REVERT: B 321 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 348 MET cc_start: 0.8916 (OUTLIER) cc_final: 0.8409 (tmm) REVERT: B 352 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8417 (mt-10) REVERT: B 393 SER cc_start: 0.8961 (m) cc_final: 0.8507 (t) REVERT: B 446 ARG cc_start: 0.8503 (mtp85) cc_final: 0.8252 (mmm-85) REVERT: B 483 GLU cc_start: 0.8992 (mp0) cc_final: 0.8607 (mp0) REVERT: B 603 GLU cc_start: 0.8818 (tt0) cc_final: 0.7842 (tt0) REVERT: B 610 LYS cc_start: 0.9032 (ttpp) cc_final: 0.8502 (ttpp) REVERT: B 612 TYR cc_start: 0.8757 (m-80) cc_final: 0.8101 (m-80) REVERT: B 624 PHE cc_start: 0.9202 (m-80) cc_final: 0.8740 (m-80) REVERT: B 686 ARG cc_start: 0.8395 (mtp-110) cc_final: 0.8015 (mtp-110) REVERT: C 103 LYS cc_start: 0.4629 (pmtt) cc_final: 0.3471 (mmmt) REVERT: D 56 MET cc_start: 0.2442 (ptp) cc_final: 0.2015 (tpt) REVERT: D 74 MET cc_start: 0.2369 (pp-130) cc_final: 0.1509 (ptt) REVERT: D 105 TYR cc_start: -0.1048 (OUTLIER) cc_final: -0.1345 (p90) REVERT: E 34 MET cc_start: 0.6371 (mtm) cc_final: 0.6136 (pp-130) outliers start: 32 outliers final: 18 residues processed: 321 average time/residue: 0.5720 time to fit residues: 204.7159 Evaluate side-chains 316 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 292 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 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 570 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 443 THR 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 D residue 103 LYS 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: 7.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 185 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 189 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 82 optimal weight: 0.7980 chunk 163 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 114 optimal weight: 0.0970 overall best weight: 1.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 180 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 668 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100830 restraints weight = 23336.229| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.84 r_work: 0.2783 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2619 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2619 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 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 = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17067 Z= 0.206 Angle : 0.670 13.318 23058 Z= 0.336 Chirality : 0.044 0.234 2468 Planarity : 0.003 0.057 2935 Dihedral : 9.973 176.858 2331 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.68 % Allowed : 22.95 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.19), residues: 2016 helix: 1.48 (0.15), residues: 1171 sheet: -0.35 (0.38), residues: 173 loop : 0.30 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 235 TYR 0.021 0.001 TYR D 105 PHE 0.015 0.001 PHE B 492 TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00471 (17066) covalent geometry : angle 0.66983 (23056) SS BOND : bond 0.00085 ( 1) SS BOND : angle 0.95689 ( 2) hydrogen bonds : bond 0.03621 ( 908) hydrogen bonds : angle 4.71677 ( 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 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 278 time to evaluate : 0.673 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: 0.9220 (t80) cc_final: 0.8954 (t80) REVERT: A 44 ASN cc_start: 0.9455 (m-40) cc_final: 0.9047 (m-40) REVERT: A 66 GLU cc_start: 0.8621 (tp30) cc_final: 0.8276 (tp30) REVERT: A 110 ASP cc_start: 0.9305 (OUTLIER) cc_final: 0.8671 (p0) REVERT: A 246 SER cc_start: 0.8132 (m) cc_final: 0.7826 (p) REVERT: A 274 ARG cc_start: 0.7757 (ptp-110) cc_final: 0.7426 (ttm-80) REVERT: A 286 ASP cc_start: 0.8984 (m-30) cc_final: 0.8247 (m-30) REVERT: A 318 ASP cc_start: 0.8996 (t0) cc_final: 0.8671 (t70) REVERT: A 362 ASP cc_start: 0.8751 (m-30) cc_final: 0.8203 (m-30) REVERT: A 384 GLU cc_start: 0.9369 (OUTLIER) cc_final: 0.9055 (pp20) REVERT: A 393 SER cc_start: 0.9157 (m) cc_final: 0.8745 (t) REVERT: A 446 ARG cc_start: 0.7583 (mmp-170) cc_final: 0.7327 (mmp-170) REVERT: A 570 MET cc_start: 0.9463 (OUTLIER) cc_final: 0.9242 (mtm) REVERT: A 583 SER cc_start: 0.9573 (t) cc_final: 0.9298 (t) REVERT: A 686 ARG cc_start: 0.8537 (mtp85) cc_final: 0.8193 (mtp85) REVERT: B 66 GLU cc_start: 0.8667 (tp30) cc_final: 0.8404 (tp30) REVERT: B 99 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9044 (mptp) REVERT: B 274 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8277 (ttm-80) REVERT: B 296 LYS cc_start: 0.8945 (mtpm) cc_final: 0.8728 (mtpp) REVERT: B 318 ASP cc_start: 0.8922 (t0) cc_final: 0.8620 (t0) REVERT: B 321 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 348 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8607 (tmm) REVERT: B 352 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8491 (mt-10) REVERT: B 393 SER cc_start: 0.9108 (m) cc_final: 0.8641 (t) REVERT: B 446 ARG cc_start: 0.8614 (mtp85) cc_final: 0.8392 (mmm-85) REVERT: B 483 GLU cc_start: 0.9122 (mp0) cc_final: 0.8721 (mp0) REVERT: B 603 GLU cc_start: 0.9056 (tt0) cc_final: 0.8367 (mt-10) REVERT: B 610 LYS cc_start: 0.9035 (ttpp) cc_final: 0.8731 (ttpp) REVERT: B 612 TYR cc_start: 0.8962 (m-80) cc_final: 0.8400 (m-80) REVERT: B 624 PHE cc_start: 0.9296 (m-80) cc_final: 0.8846 (m-80) REVERT: B 686 ARG cc_start: 0.8612 (mtp-110) cc_final: 0.8187 (mtp-110) REVERT: C 103 LYS cc_start: 0.4532 (pmtt) cc_final: 0.3477 (mmmt) REVERT: C 146 GLN cc_start: 0.8123 (mm-40) cc_final: 0.7833 (mm-40) REVERT: D 56 MET cc_start: 0.2485 (ptp) cc_final: 0.2023 (tpt) REVERT: D 74 MET cc_start: 0.2056 (pp-130) cc_final: 0.1847 (pp-130) REVERT: D 105 TYR cc_start: -0.0793 (OUTLIER) cc_final: -0.1130 (p90) REVERT: E 34 MET cc_start: 0.6436 (mtm) cc_final: 0.6127 (pp-130) outliers start: 30 outliers final: 19 residues processed: 292 average time/residue: 0.5677 time to fit residues: 183.8074 Evaluate side-chains 299 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 274 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 570 MET 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 A residue 687 THR Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR 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 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: 9.9990 chunk 54 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 171 optimal weight: 40.0000 chunk 43 optimal weight: 0.9980 chunk 160 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 chunk 125 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 238 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 = 0.4107 r_free = 0.4107 target = 0.187437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.101762 restraints weight = 23365.461| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.84 r_work: 0.2804 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2649 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2649 r_free = 0.2649 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 = 0.2649 r_free = 0.2649 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2649 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17067 Z= 0.157 Angle : 0.651 13.163 23058 Z= 0.326 Chirality : 0.043 0.232 2468 Planarity : 0.003 0.057 2935 Dihedral : 9.814 176.333 2331 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.56 % Allowed : 23.06 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.19), residues: 2016 helix: 1.53 (0.15), residues: 1167 sheet: -0.45 (0.37), residues: 173 loop : 0.36 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 235 TYR 0.020 0.001 TYR D 105 PHE 0.015 0.001 PHE C 227 TRP 0.007 0.001 TRP B 9 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00359 (17066) covalent geometry : angle 0.65096 (23056) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.95015 ( 2) hydrogen bonds : bond 0.03502 ( 908) hydrogen bonds : angle 4.65859 ( 2676) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9198.47 seconds wall clock time: 156 minutes 39.63 seconds (9399.63 seconds total)