Starting phenix.real_space_refine on Sat Jun 14 21:15:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byl_45037/06_2025/9byl_45037_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byl_45037/06_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_45037/06_2025/9byl_45037.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byl_45037/06_2025/9byl_45037.map" model { file = "/net/cci-nas-00/data/ceres_data/9byl_45037/06_2025/9byl_45037_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byl_45037/06_2025/9byl_45037_neut.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.46, per 1000 atoms: 0.63 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: 4.79 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.71 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: 5.88 Time building geometry restraints manager: 5.57 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 41.060 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.410 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (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 TRP 0.077 0.005 TRP E 25 HIS 0.006 0.001 HIS C 254 PHE 0.031 0.003 PHE B 24 TYR 0.029 0.002 TYR E 67 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15639 ( 908) hydrogen bonds : angle 6.57691 ( 2676) SS BOND : bond 0.62925 ( 1) SS BOND : angle 9.71235 ( 2) covalent geometry : bond 0.00597 (17066) covalent geometry : angle 0.80194 (23056) *********************** 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 : 2.160 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: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.7889 (p0) REVERT: A 246 SER cc_start: 0.8197 (m) cc_final: 0.7978 (p) REVERT: A 447 ASN cc_start: 0.8023 (m-40) cc_final: 0.7654 (m-40) outliers start: 26 outliers final: 8 residues processed: 492 average time/residue: 1.3645 time to fit residues: 742.5423 Evaluate side-chains 328 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 319 time to evaluate : 1.885 ------------------------------------------------------------------------------- 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 168 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 156 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 181 optimal weight: 10.0000 overall best weight: 0.8560 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 38 ASN C 84 HIS C 119 ASN C 238 ASN D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.100550 restraints weight = 22476.526| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.75 r_work: 0.2802 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17067 Z= 0.160 Angle : 0.601 12.439 23058 Z= 0.312 Chirality : 0.042 0.212 2468 Planarity : 0.003 0.043 2935 Dihedral : 11.238 179.397 2345 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.63 % Allowed : 17.76 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.18), residues: 2016 helix: 1.62 (0.15), residues: 1165 sheet: 0.36 (0.40), residues: 157 loop : 0.60 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.006 0.001 HIS A 438 PHE 0.017 0.001 PHE B 100 TYR 0.020 0.001 TYR D 105 ARG 0.008 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 908) hydrogen bonds : angle 4.92581 ( 2676) SS BOND : bond 0.00575 ( 1) SS BOND : angle 2.16686 ( 2) covalent geometry : bond 0.00352 (17066) covalent geometry : angle 0.60092 (23056) *********************** 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 388 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 323 time to evaluate : 1.903 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: 0.9233 (m-30) cc_final: 0.8951 (m-30) REVERT: A 66 GLU cc_start: 0.8673 (tp30) cc_final: 0.8317 (tp30) REVERT: A 103 ASP cc_start: 0.9189 (m-30) cc_final: 0.8864 (m-30) REVERT: A 110 ASP cc_start: 0.9376 (OUTLIER) cc_final: 0.8702 (p0) REVERT: A 194 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8939 (ttmm) REVERT: A 246 SER cc_start: 0.8127 (m) cc_final: 0.7759 (p) REVERT: A 270 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.7932 (OUTLIER) REVERT: A 274 ARG cc_start: 0.8213 (ptp-110) cc_final: 0.7952 (ptp-110) REVERT: A 286 ASP cc_start: 0.8943 (m-30) cc_final: 0.8367 (m-30) REVERT: A 362 ASP cc_start: 0.8665 (m-30) cc_final: 0.8268 (m-30) REVERT: A 384 GLU cc_start: 0.9324 (OUTLIER) cc_final: 0.8683 (pp20) REVERT: A 421 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 446 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6763 (mmp-170) REVERT: A 583 SER cc_start: 0.9261 (OUTLIER) cc_final: 0.9028 (t) REVERT: A 686 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7832 (mtp85) REVERT: B 23 LYS cc_start: 0.8836 (mtmm) cc_final: 0.8530 (mttp) REVERT: B 104 TYR cc_start: 0.9111 (m-80) cc_final: 0.8809 (m-80) REVERT: B 139 GLU cc_start: 0.9191 (mt-10) cc_final: 0.8935 (mt-10) REVERT: B 274 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7767 (ttm110) REVERT: B 393 SER cc_start: 0.9058 (m) cc_final: 0.8647 (t) REVERT: B 483 GLU cc_start: 0.9041 (mp0) cc_final: 0.8631 (mp0) REVERT: B 603 GLU cc_start: 0.9092 (tt0) cc_final: 0.8516 (mt-10) REVERT: B 612 TYR cc_start: 0.9064 (m-80) cc_final: 0.8639 (m-80) REVERT: B 624 PHE cc_start: 0.9105 (m-80) cc_final: 0.8706 (m-80) REVERT: C 85 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: C 137 MET cc_start: 0.1100 (mtp) cc_final: 0.0846 (mmp) REVERT: D 56 MET cc_start: 0.2240 (ptp) cc_final: 0.1967 (tpt) REVERT: D 235 LEU cc_start: 0.7662 (mt) cc_final: 0.7461 (pp) outliers start: 65 outliers final: 19 residues processed: 363 average time/residue: 1.3432 time to fit residues: 541.3531 Evaluate side-chains 305 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 2.167 ------------------------------------------------------------------------------- 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 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 174 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 113 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN D 132 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.185902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.098674 restraints weight = 22812.976| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.71 r_work: 0.2730 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 17067 Z= 0.254 Angle : 0.615 10.571 23058 Z= 0.316 Chirality : 0.043 0.170 2468 Planarity : 0.003 0.042 2935 Dihedral : 11.144 179.128 2335 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.52 % Allowed : 18.09 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2016 helix: 1.56 (0.15), residues: 1175 sheet: 0.34 (0.40), residues: 157 loop : 0.45 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 PHE 0.016 0.002 PHE B 492 TYR 0.021 0.002 TYR D 105 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04246 ( 908) hydrogen bonds : angle 4.78006 ( 2676) SS BOND : bond 0.00174 ( 1) SS BOND : angle 1.66706 ( 2) covalent geometry : bond 0.00572 (17066) covalent geometry : angle 0.61460 (23056) *********************** 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 341 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 278 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.9211 (m-30) cc_final: 0.9000 (m-30) REVERT: A 66 GLU cc_start: 0.8721 (tp30) cc_final: 0.8451 (tp30) REVERT: A 103 ASP cc_start: 0.9224 (m-30) cc_final: 0.8907 (m-30) REVERT: A 110 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.8635 (p0) REVERT: A 246 SER cc_start: 0.8253 (m) cc_final: 0.7878 (p) REVERT: A 270 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8012 (OUTLIER) REVERT: A 286 ASP cc_start: 0.8978 (m-30) cc_final: 0.8479 (m-30) REVERT: A 362 ASP cc_start: 0.8741 (m-30) cc_final: 0.8381 (m-30) REVERT: A 384 GLU cc_start: 0.9477 (OUTLIER) cc_final: 0.8705 (pp20) REVERT: A 393 SER cc_start: 0.9122 (m) cc_final: 0.8678 (t) REVERT: A 445 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 583 SER cc_start: 0.9508 (t) cc_final: 0.9232 (t) REVERT: B 104 TYR cc_start: 0.9198 (m-80) cc_final: 0.8924 (m-80) REVERT: B 139 GLU cc_start: 0.9267 (mt-10) cc_final: 0.9013 (mt-10) REVERT: B 274 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.8002 (ttm110) REVERT: B 384 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.8666 (pp20) REVERT: B 483 GLU cc_start: 0.9135 (mp0) cc_final: 0.8736 (mp0) REVERT: B 603 GLU cc_start: 0.9059 (tt0) cc_final: 0.8499 (mt-10) REVERT: B 612 TYR cc_start: 0.9115 (m-80) cc_final: 0.8665 (m-80) REVERT: B 624 PHE cc_start: 0.9250 (m-80) cc_final: 0.8867 (m-80) REVERT: B 686 ARG cc_start: 0.8725 (mtp-110) cc_final: 0.8344 (mtp-110) REVERT: C 96 MET cc_start: 0.7824 (tpp) cc_final: 0.6888 (mmt) REVERT: C 123 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7955 (tp30) REVERT: C 137 MET cc_start: 0.1448 (mtp) cc_final: 0.1238 (mmp) REVERT: D 56 MET cc_start: 0.2270 (ptp) cc_final: 0.1823 (tpt) REVERT: D 105 TYR cc_start: -0.1550 (OUTLIER) cc_final: -0.1889 (p90) outliers start: 63 outliers final: 25 residues processed: 319 average time/residue: 1.5400 time to fit residues: 546.6683 Evaluate side-chains 290 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 260 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 107 LYS 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 241 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 102 optimal weight: 0.8980 chunk 156 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 158 optimal weight: 40.0000 chunk 76 optimal weight: 0.0770 chunk 167 optimal weight: 30.0000 chunk 49 optimal weight: 0.6980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN ** D 265 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 = 0.4107 r_free = 0.4107 target = 0.189058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101889 restraints weight = 22633.577| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.83 r_work: 0.2798 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 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 = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17067 Z= 0.138 Angle : 0.583 11.566 23058 Z= 0.296 Chirality : 0.041 0.166 2468 Planarity : 0.003 0.042 2935 Dihedral : 10.752 177.941 2335 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.24 % Allowed : 19.10 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.18), residues: 2016 helix: 1.58 (0.15), residues: 1173 sheet: 0.20 (0.39), residues: 153 loop : 0.34 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.006 0.001 HIS C 201 PHE 0.017 0.001 PHE A 100 TYR 0.024 0.001 TYR D 105 ARG 0.011 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 908) hydrogen bonds : angle 4.63752 ( 2676) SS BOND : bond 0.00180 ( 1) SS BOND : angle 1.39934 ( 2) covalent geometry : bond 0.00303 (17066) covalent geometry : angle 0.58322 (23056) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 300 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8717 (tp30) cc_final: 0.8421 (tp30) REVERT: A 103 ASP cc_start: 0.9228 (m-30) cc_final: 0.8934 (m-30) REVERT: A 110 ASP cc_start: 0.9353 (OUTLIER) cc_final: 0.9047 (p0) REVERT: A 184 ARG cc_start: 0.9018 (ttm-80) cc_final: 0.8704 (tpp-160) REVERT: A 246 SER cc_start: 0.8225 (m) cc_final: 0.7893 (p) REVERT: A 355 TYR cc_start: 0.9144 (m-10) cc_final: 0.8908 (m-10) REVERT: A 362 ASP cc_start: 0.8748 (m-30) cc_final: 0.8473 (m-30) REVERT: A 384 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.8547 (pp20) REVERT: A 393 SER cc_start: 0.9062 (m) cc_final: 0.8593 (t) REVERT: A 413 SER cc_start: 0.9475 (OUTLIER) cc_final: 0.9111 (p) REVERT: A 445 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8946 (mm) REVERT: A 583 SER cc_start: 0.9503 (t) cc_final: 0.9241 (t) REVERT: A 686 ARG cc_start: 0.8502 (mtp-110) cc_final: 0.8248 (mtp-110) REVERT: B 53 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8872 (mp0) REVERT: B 104 TYR cc_start: 0.9142 (m-80) cc_final: 0.8894 (m-80) REVERT: B 217 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8607 (mm-30) REVERT: B 235 ARG cc_start: 0.9021 (ttm-80) cc_final: 0.8539 (ttm-80) REVERT: B 274 ARG cc_start: 0.8343 (ttm-80) cc_final: 0.8011 (ttm110) REVERT: B 336 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.8997 (ttmm) REVERT: B 348 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8535 (tmm) REVERT: B 393 SER cc_start: 0.9139 (m) cc_final: 0.8754 (t) REVERT: B 483 GLU cc_start: 0.9104 (mp0) cc_final: 0.8719 (mp0) REVERT: B 603 GLU cc_start: 0.9103 (tt0) cc_final: 0.8560 (mt-10) REVERT: B 610 LYS cc_start: 0.8960 (ttpp) cc_final: 0.8639 (ttmm) REVERT: B 612 TYR cc_start: 0.9015 (m-80) cc_final: 0.8622 (m-80) REVERT: B 624 PHE cc_start: 0.9158 (m-80) cc_final: 0.8768 (m-80) REVERT: B 686 ARG cc_start: 0.8674 (mtp-110) cc_final: 0.8289 (mtp-110) REVERT: C 85 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: C 123 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7920 (tp30) REVERT: D 56 MET cc_start: 0.2351 (ptp) cc_final: 0.1912 (tpt) REVERT: D 105 TYR cc_start: -0.1396 (OUTLIER) cc_final: -0.1696 (p90) outliers start: 58 outliers final: 24 residues processed: 332 average time/residue: 1.3532 time to fit residues: 498.1738 Evaluate side-chains 312 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 1.946 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU 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 408 SER 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 127 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 241 GLU 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 E residue 98 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 182 optimal weight: 50.0000 chunk 76 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.187674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.104208 restraints weight = 22782.279| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 2.73 r_work: 0.2783 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 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 = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17067 Z= 0.171 Angle : 0.583 10.777 23058 Z= 0.296 Chirality : 0.042 0.210 2468 Planarity : 0.003 0.046 2935 Dihedral : 10.560 177.813 2333 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.18 % Allowed : 19.88 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.18), residues: 2016 helix: 1.56 (0.15), residues: 1176 sheet: -0.03 (0.37), residues: 165 loop : 0.32 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.005 0.001 HIS C 201 PHE 0.015 0.001 PHE B 100 TYR 0.026 0.001 TYR D 174 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 908) hydrogen bonds : angle 4.62042 ( 2676) SS BOND : bond 0.00143 ( 1) SS BOND : angle 1.24822 ( 2) covalent geometry : bond 0.00384 (17066) covalent geometry : angle 0.58266 (23056) *********************** 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 344 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 1.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.9235 (m-30) cc_final: 0.9021 (m-30) REVERT: A 66 GLU cc_start: 0.8707 (tp30) cc_final: 0.8368 (tp30) REVERT: A 103 ASP cc_start: 0.9210 (m-30) cc_final: 0.8937 (m-30) REVERT: A 110 ASP cc_start: 0.9358 (OUTLIER) cc_final: 0.8655 (p0) REVERT: A 184 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8779 (tpp-160) REVERT: A 194 LYS cc_start: 0.9303 (OUTLIER) cc_final: 0.8884 (ttmm) REVERT: A 246 SER cc_start: 0.8182 (m) cc_final: 0.7851 (p) REVERT: A 362 ASP cc_start: 0.8726 (m-30) cc_final: 0.8460 (m-30) REVERT: A 384 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.8645 (pp20) REVERT: A 393 SER cc_start: 0.9057 (m) cc_final: 0.8592 (t) REVERT: A 445 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8905 (mm) REVERT: A 452 ARG cc_start: 0.9255 (ttp80) cc_final: 0.9014 (ttp80) REVERT: A 583 SER cc_start: 0.9534 (t) cc_final: 0.9265 (t) REVERT: A 677 ARG cc_start: 0.9223 (OUTLIER) cc_final: 0.8710 (mmm160) REVERT: A 686 ARG cc_start: 0.8503 (mtp-110) cc_final: 0.8132 (mtp-110) REVERT: B 53 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8861 (mp0) REVERT: B 104 TYR cc_start: 0.9193 (m-80) cc_final: 0.8798 (m-80) REVERT: B 221 LYS cc_start: 0.9353 (mttm) cc_final: 0.9105 (mttm) REVERT: B 235 ARG cc_start: 0.9102 (ttm-80) cc_final: 0.8883 (ttm-80) REVERT: B 274 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8058 (ttm110) REVERT: B 336 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9104 (ttmm) REVERT: B 348 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8570 (tmm) REVERT: B 393 SER cc_start: 0.9131 (m) cc_final: 0.8761 (t) REVERT: B 396 ASP cc_start: 0.9001 (m-30) cc_final: 0.8718 (m-30) REVERT: B 483 GLU cc_start: 0.9118 (mp0) cc_final: 0.8704 (mp0) REVERT: B 603 GLU cc_start: 0.9051 (tt0) cc_final: 0.8473 (mt-10) REVERT: B 610 LYS cc_start: 0.9001 (ttpp) cc_final: 0.8633 (ttmm) REVERT: B 612 TYR cc_start: 0.9013 (m-80) cc_final: 0.8608 (m-80) REVERT: B 624 PHE cc_start: 0.9218 (m-80) cc_final: 0.8799 (m-80) REVERT: B 686 ARG cc_start: 0.8639 (mtp-110) cc_final: 0.8297 (mtp-110) REVERT: C 85 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: D 56 MET cc_start: 0.2660 (ptp) cc_final: 0.2246 (tpt) REVERT: D 105 TYR cc_start: -0.1284 (OUTLIER) cc_final: -0.1587 (p90) outliers start: 57 outliers final: 22 residues processed: 321 average time/residue: 1.3167 time to fit residues: 469.2536 Evaluate side-chains 301 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 270 time to evaluate : 1.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 408 SER 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 241 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 11 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 668 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.185829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099946 restraints weight = 23396.491| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.93 r_work: 0.2768 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17067 Z= 0.161 Angle : 0.580 11.157 23058 Z= 0.295 Chirality : 0.042 0.211 2468 Planarity : 0.003 0.048 2935 Dihedral : 10.400 176.879 2333 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.13 % Allowed : 20.66 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2016 helix: 1.55 (0.15), residues: 1177 sheet: -0.26 (0.37), residues: 173 loop : 0.29 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.006 0.001 HIS D 101 PHE 0.015 0.001 PHE B 100 TYR 0.027 0.001 TYR D 174 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 908) hydrogen bonds : angle 4.59250 ( 2676) SS BOND : bond 0.00113 ( 1) SS BOND : angle 1.12824 ( 2) covalent geometry : bond 0.00360 (17066) covalent geometry : angle 0.57977 (23056) *********************** 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 359 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 303 time to evaluate : 2.088 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: A 40 TYR cc_start: 0.9056 (t80) cc_final: 0.8840 (t80) REVERT: A 44 ASN cc_start: 0.9350 (m-40) cc_final: 0.8932 (m-40) REVERT: A 66 GLU cc_start: 0.8522 (tp30) cc_final: 0.8155 (tp30) REVERT: A 103 ASP cc_start: 0.9104 (m-30) cc_final: 0.8797 (m-30) REVERT: A 110 ASP cc_start: 0.9334 (OUTLIER) cc_final: 0.8610 (p0) REVERT: A 194 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8699 (ttmm) REVERT: A 246 SER cc_start: 0.7851 (m) cc_final: 0.7540 (p) REVERT: A 286 ASP cc_start: 0.8847 (m-30) cc_final: 0.8026 (m-30) REVERT: A 362 ASP cc_start: 0.8470 (m-30) cc_final: 0.7832 (m-30) REVERT: A 384 GLU cc_start: 0.9364 (OUTLIER) cc_final: 0.8368 (pp20) REVERT: A 393 SER cc_start: 0.9002 (m) cc_final: 0.8537 (t) REVERT: A 445 ILE cc_start: 0.9336 (OUTLIER) cc_final: 0.8916 (mm) REVERT: A 452 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8809 (ttp80) REVERT: A 583 SER cc_start: 0.9434 (t) cc_final: 0.9180 (t) REVERT: A 677 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8625 (mmm160) REVERT: B 104 TYR cc_start: 0.9170 (m-80) cc_final: 0.8727 (m-80) REVERT: B 221 LYS cc_start: 0.9240 (mttm) cc_final: 0.8941 (mttm) REVERT: B 235 ARG cc_start: 0.8932 (ttm-80) cc_final: 0.8698 (ttm-80) REVERT: B 274 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.8006 (ttm110) REVERT: B 348 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8356 (tmm) REVERT: B 393 SER cc_start: 0.9012 (m) cc_final: 0.8579 (t) REVERT: B 396 ASP cc_start: 0.8815 (m-30) cc_final: 0.8534 (m-30) REVERT: B 483 GLU cc_start: 0.8994 (mp0) cc_final: 0.8532 (mp0) REVERT: B 603 GLU cc_start: 0.8950 (tt0) cc_final: 0.8405 (mt-10) REVERT: B 610 LYS cc_start: 0.8998 (ttpp) cc_final: 0.8604 (ttmm) REVERT: B 612 TYR cc_start: 0.8907 (m-80) cc_final: 0.8522 (m-80) REVERT: B 624 PHE cc_start: 0.9167 (m-80) cc_final: 0.8656 (m-80) REVERT: B 686 ARG cc_start: 0.8470 (mtp-110) cc_final: 0.8072 (mtp-110) REVERT: C 85 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: D 56 MET cc_start: 0.2458 (ptp) cc_final: 0.2045 (tpt) REVERT: D 74 MET cc_start: 0.2487 (OUTLIER) cc_final: 0.2077 (ptt) REVERT: D 105 TYR cc_start: -0.1231 (OUTLIER) cc_final: -0.1528 (p90) REVERT: E 34 MET cc_start: 0.6353 (mtm) cc_final: 0.6146 (pp-130) outliers start: 56 outliers final: 27 residues processed: 337 average time/residue: 1.3120 time to fit residues: 491.3216 Evaluate side-chains 318 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 282 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 677 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 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 46 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 176 optimal weight: 50.0000 chunk 166 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 163 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 127 optimal weight: 0.0770 chunk 23 optimal weight: 5.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.187021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.101706 restraints weight = 23186.134| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.90 r_work: 0.2794 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2635 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2635 ------------------------------------------------------------------------------- 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: 0.8041 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17067 Z= 0.134 Angle : 0.588 11.676 23058 Z= 0.298 Chirality : 0.041 0.205 2468 Planarity : 0.003 0.052 2935 Dihedral : 10.210 178.347 2333 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.68 % Allowed : 21.27 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 2016 helix: 1.57 (0.15), residues: 1173 sheet: -0.19 (0.37), residues: 169 loop : 0.26 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.005 0.001 HIS D 101 PHE 0.016 0.001 PHE A 100 TYR 0.021 0.001 TYR D 105 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 908) hydrogen bonds : angle 4.56110 ( 2676) SS BOND : bond 0.00084 ( 1) SS BOND : angle 1.03017 ( 2) covalent geometry : bond 0.00300 (17066) covalent geometry : angle 0.58834 (23056) *********************** 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 351 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 303 time to evaluate : 2.880 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: A 39 ASP cc_start: 0.9245 (m-30) cc_final: 0.9023 (m-30) REVERT: A 40 TYR cc_start: 0.9153 (t80) cc_final: 0.8918 (t80) REVERT: A 44 ASN cc_start: 0.9385 (m-40) cc_final: 0.8977 (m-40) REVERT: A 66 GLU cc_start: 0.8682 (tp30) cc_final: 0.8300 (tp30) REVERT: A 99 LYS cc_start: 0.8920 (mmtt) cc_final: 0.8607 (mmtp) REVERT: A 103 ASP cc_start: 0.9260 (m-30) cc_final: 0.9028 (m-30) REVERT: A 110 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.8553 (p0) REVERT: A 119 GLU cc_start: 0.9128 (mp0) cc_final: 0.8905 (mp0) REVERT: A 194 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8788 (ttmm) REVERT: A 246 SER cc_start: 0.8028 (m) cc_final: 0.7727 (p) REVERT: A 274 ARG cc_start: 0.7850 (ptp-110) cc_final: 0.7552 (ttm110) REVERT: A 286 ASP cc_start: 0.9008 (m-30) cc_final: 0.8324 (m-30) REVERT: A 362 ASP cc_start: 0.8727 (m-30) cc_final: 0.8116 (m-30) REVERT: A 384 GLU cc_start: 0.9386 (OUTLIER) cc_final: 0.8455 (pp20) REVERT: A 393 SER cc_start: 0.8946 (m) cc_final: 0.8481 (t) REVERT: A 413 SER cc_start: 0.9495 (OUTLIER) cc_final: 0.9269 (p) REVERT: A 445 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.8950 (mm) REVERT: A 452 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8924 (ttp80) REVERT: A 597 ILE cc_start: 0.9538 (pt) cc_final: 0.9292 (pp) REVERT: B 104 TYR cc_start: 0.9221 (m-80) cc_final: 0.8628 (m-80) REVERT: B 221 LYS cc_start: 0.9238 (mttm) cc_final: 0.8957 (mttm) REVERT: B 235 ARG cc_start: 0.9068 (ttm-80) cc_final: 0.8761 (ttm-80) REVERT: B 246 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.7756 (p) REVERT: B 274 ARG cc_start: 0.8334 (ttm-80) cc_final: 0.7950 (ttm110) REVERT: B 296 LYS cc_start: 0.8778 (mtpm) cc_final: 0.8557 (mtpp) REVERT: B 321 GLU cc_start: 0.9073 (pt0) cc_final: 0.8826 (pt0) REVERT: B 348 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8582 (tmm) REVERT: B 393 SER cc_start: 0.9035 (m) cc_final: 0.8613 (t) REVERT: B 420 MET cc_start: 0.9539 (mmm) cc_final: 0.9312 (mmp) REVERT: B 483 GLU cc_start: 0.9047 (mp0) cc_final: 0.8626 (mp0) REVERT: B 603 GLU cc_start: 0.9100 (tt0) cc_final: 0.8570 (mt-10) REVERT: B 610 LYS cc_start: 0.9029 (ttpp) cc_final: 0.8651 (ttpp) REVERT: B 612 TYR cc_start: 0.8916 (m-80) cc_final: 0.8456 (m-80) REVERT: B 624 PHE cc_start: 0.9223 (m-80) cc_final: 0.8760 (m-80) REVERT: B 686 ARG cc_start: 0.8531 (mtp-110) cc_final: 0.8159 (mtp-110) REVERT: C 85 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6461 (tm-30) REVERT: D 56 MET cc_start: 0.2507 (ptp) cc_final: 0.2082 (tpt) REVERT: D 74 MET cc_start: 0.2763 (OUTLIER) cc_final: 0.2464 (ptt) REVERT: D 105 TYR cc_start: -0.1127 (OUTLIER) cc_final: -0.1413 (p90) REVERT: E 34 MET cc_start: 0.6420 (mtm) cc_final: 0.6137 (pp-130) outliers start: 48 outliers final: 24 residues processed: 329 average time/residue: 1.4783 time to fit residues: 539.9270 Evaluate side-chains 312 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 278 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS 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 B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 408 SER 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 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 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 88 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 157 optimal weight: 30.0000 chunk 184 optimal weight: 6.9990 chunk 151 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 65 optimal weight: 0.1980 chunk 190 optimal weight: 0.0570 chunk 45 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 668 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.187186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.103185 restraints weight = 23240.329| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.94 r_work: 0.2823 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2663 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17067 Z= 0.130 Angle : 0.594 12.238 23058 Z= 0.300 Chirality : 0.041 0.211 2468 Planarity : 0.003 0.054 2935 Dihedral : 9.965 178.201 2333 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.40 % Allowed : 21.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.19), residues: 2016 helix: 1.56 (0.15), residues: 1171 sheet: -0.21 (0.37), residues: 169 loop : 0.26 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.011 0.001 HIS C 201 PHE 0.014 0.001 PHE B 100 TYR 0.020 0.001 TYR D 105 ARG 0.010 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03439 ( 908) hydrogen bonds : angle 4.55186 ( 2676) SS BOND : bond 0.00095 ( 1) SS BOND : angle 1.00915 ( 2) covalent geometry : bond 0.00291 (17066) covalent geometry : angle 0.59377 (23056) *********************** 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 336 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 293 time to evaluate : 2.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9156 (t80) cc_final: 0.8872 (t80) REVERT: A 44 ASN cc_start: 0.9382 (m-40) cc_final: 0.8935 (m-40) REVERT: A 66 GLU cc_start: 0.8689 (tp30) cc_final: 0.8268 (tp30) REVERT: A 99 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8590 (tptp) REVERT: A 103 ASP cc_start: 0.9264 (m-30) cc_final: 0.9034 (m-30) REVERT: A 110 ASP cc_start: 0.9258 (OUTLIER) cc_final: 0.8867 (p0) REVERT: A 119 GLU cc_start: 0.9120 (mp0) cc_final: 0.8903 (mp0) REVERT: A 194 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8752 (ttmm) REVERT: A 246 SER cc_start: 0.8019 (m) cc_final: 0.7690 (p) REVERT: A 286 ASP cc_start: 0.8997 (m-30) cc_final: 0.8326 (m-30) REVERT: A 362 ASP cc_start: 0.8707 (m-30) cc_final: 0.8076 (m-30) REVERT: A 384 GLU cc_start: 0.9338 (OUTLIER) cc_final: 0.8387 (pp20) REVERT: A 393 SER cc_start: 0.8943 (m) cc_final: 0.8507 (t) REVERT: A 413 SER cc_start: 0.9409 (OUTLIER) cc_final: 0.9182 (p) REVERT: A 445 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.8960 (mm) REVERT: A 452 ARG cc_start: 0.9192 (ttp80) cc_final: 0.8972 (ttp80) REVERT: A 597 ILE cc_start: 0.9561 (pt) cc_final: 0.9347 (pp) REVERT: B 104 TYR cc_start: 0.9216 (m-80) cc_final: 0.8627 (m-80) REVERT: B 221 LYS cc_start: 0.9259 (mttm) cc_final: 0.9006 (mttm) REVERT: B 235 ARG cc_start: 0.9071 (ttm-80) cc_final: 0.8748 (ttm-80) REVERT: B 246 SER cc_start: 0.8376 (OUTLIER) cc_final: 0.7764 (p) REVERT: B 274 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8024 (ttm110) REVERT: B 296 LYS cc_start: 0.8859 (mtpm) cc_final: 0.8540 (ptpp) REVERT: B 321 GLU cc_start: 0.9034 (pt0) cc_final: 0.8797 (pt0) REVERT: B 348 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8525 (tmm) REVERT: B 352 GLU cc_start: 0.9025 (mt-10) cc_final: 0.8604 (mt-10) REVERT: B 393 SER cc_start: 0.9030 (m) cc_final: 0.8577 (t) REVERT: B 420 MET cc_start: 0.9524 (mmm) cc_final: 0.9323 (mmp) REVERT: B 483 GLU cc_start: 0.9040 (mp0) cc_final: 0.8604 (mp0) REVERT: B 570 MET cc_start: 0.9621 (mtm) cc_final: 0.9383 (mtm) REVERT: B 586 TYR cc_start: 0.9194 (m-80) cc_final: 0.8829 (m-80) REVERT: B 603 GLU cc_start: 0.9076 (tt0) cc_final: 0.8455 (mt-10) REVERT: B 610 LYS cc_start: 0.9030 (ttpp) cc_final: 0.8644 (ttpp) REVERT: B 612 TYR cc_start: 0.8851 (m-80) cc_final: 0.8362 (m-80) REVERT: B 624 PHE cc_start: 0.9239 (m-80) cc_final: 0.8793 (m-80) REVERT: B 686 ARG cc_start: 0.8448 (mtp-110) cc_final: 0.8056 (mtp-110) REVERT: C 85 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: D 56 MET cc_start: 0.2341 (ptp) cc_final: 0.1885 (tpt) REVERT: D 74 MET cc_start: 0.2478 (OUTLIER) cc_final: 0.2005 (ptt) REVERT: D 105 TYR cc_start: -0.1005 (OUTLIER) cc_final: -0.1305 (p90) REVERT: E 34 MET cc_start: 0.6451 (mtm) cc_final: 0.6109 (pp-130) outliers start: 43 outliers final: 20 residues processed: 314 average time/residue: 1.4729 time to fit residues: 515.6193 Evaluate side-chains 314 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 408 SER 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 599 GLU 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 C residue 241 GLU Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 27 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 138 optimal weight: 50.0000 chunk 96 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.186061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100917 restraints weight = 23118.840| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.84 r_work: 0.2746 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 17067 Z= 0.232 Angle : 0.662 15.475 23058 Z= 0.333 Chirality : 0.044 0.225 2468 Planarity : 0.003 0.056 2935 Dihedral : 10.141 178.482 2332 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.18 % Allowed : 21.78 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 2016 helix: 1.52 (0.15), residues: 1170 sheet: -0.24 (0.38), residues: 165 loop : 0.28 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.007 0.001 HIS C 201 PHE 0.016 0.001 PHE A 487 TYR 0.021 0.001 TYR D 105 ARG 0.013 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03696 ( 908) hydrogen bonds : angle 4.68632 ( 2676) SS BOND : bond 0.00092 ( 1) SS BOND : angle 1.00525 ( 2) covalent geometry : bond 0.00528 (17066) covalent geometry : angle 0.66240 (23056) *********************** 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 321 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 282 time to evaluate : 2.210 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: 0.9147 (t80) cc_final: 0.8856 (t80) REVERT: A 44 ASN cc_start: 0.9377 (m-40) cc_final: 0.8951 (m-40) REVERT: A 66 GLU cc_start: 0.8686 (tp30) cc_final: 0.8306 (tp30) REVERT: A 110 ASP cc_start: 0.9248 (OUTLIER) cc_final: 0.8547 (p0) REVERT: A 194 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8738 (ttmm) REVERT: A 246 SER cc_start: 0.8015 (m) cc_final: 0.7660 (p) REVERT: A 286 ASP cc_start: 0.8982 (m-30) cc_final: 0.8191 (m-30) REVERT: A 362 ASP cc_start: 0.8754 (m-30) cc_final: 0.8157 (m-30) REVERT: A 384 GLU cc_start: 0.9423 (OUTLIER) cc_final: 0.9052 (pp20) REVERT: A 393 SER cc_start: 0.9035 (m) cc_final: 0.8590 (t) REVERT: A 439 VAL cc_start: 0.9311 (t) cc_final: 0.9034 (p) REVERT: A 445 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9139 (mm) REVERT: A 452 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8963 (ttp80) REVERT: A 539 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8812 (mmpt) REVERT: B 104 TYR cc_start: 0.9344 (m-80) cc_final: 0.8618 (m-80) REVERT: B 221 LYS cc_start: 0.9275 (mttm) cc_final: 0.9065 (mttm) REVERT: B 246 SER cc_start: 0.8406 (OUTLIER) cc_final: 0.7696 (p) REVERT: B 274 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.7996 (ttm110) REVERT: B 296 LYS cc_start: 0.8819 (mtpm) cc_final: 0.8576 (mtpp) REVERT: B 321 GLU cc_start: 0.9056 (pt0) cc_final: 0.8811 (pt0) REVERT: B 348 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8741 (tmm) REVERT: B 393 SER cc_start: 0.9054 (m) cc_final: 0.8619 (t) REVERT: B 406 ASP cc_start: 0.8846 (m-30) cc_final: 0.8642 (m-30) REVERT: B 483 GLU cc_start: 0.9082 (mp0) cc_final: 0.8668 (mp0) REVERT: B 570 MET cc_start: 0.9630 (OUTLIER) cc_final: 0.9401 (mtm) REVERT: B 603 GLU cc_start: 0.9085 (tt0) cc_final: 0.8430 (mt-10) REVERT: B 610 LYS cc_start: 0.8971 (ttpp) cc_final: 0.8677 (ttpp) REVERT: B 612 TYR cc_start: 0.8963 (m-80) cc_final: 0.8441 (m-80) REVERT: B 624 PHE cc_start: 0.9306 (m-80) cc_final: 0.8844 (m-80) REVERT: B 686 ARG cc_start: 0.8552 (mtp-110) cc_final: 0.8129 (mtp-110) REVERT: C 85 GLN cc_start: 0.6869 (OUTLIER) cc_final: 0.6406 (tm-30) REVERT: D 56 MET cc_start: 0.2318 (ptp) cc_final: 0.1878 (tpt) REVERT: D 74 MET cc_start: 0.2482 (OUTLIER) cc_final: 0.1890 (ptt) REVERT: D 105 TYR cc_start: -0.0983 (OUTLIER) cc_final: -0.1310 (p90) REVERT: E 34 MET cc_start: 0.6437 (mtm) cc_final: 0.6110 (pp-130) outliers start: 39 outliers final: 20 residues processed: 302 average time/residue: 1.3387 time to fit residues: 450.5186 Evaluate side-chains 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 277 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 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 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 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 C residue 241 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 143 optimal weight: 7.9990 chunk 9 optimal weight: 0.5980 chunk 165 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 128 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 197 optimal weight: 30.0000 chunk 125 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 164 optimal weight: 40.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.187566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.102782 restraints weight = 23188.487| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.77 r_work: 0.2780 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 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 = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17067 Z= 0.170 Angle : 0.652 13.109 23058 Z= 0.326 Chirality : 0.043 0.246 2468 Planarity : 0.003 0.054 2935 Dihedral : 9.976 178.479 2332 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.90 % Allowed : 22.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 2016 helix: 1.54 (0.15), residues: 1167 sheet: -0.40 (0.37), residues: 169 loop : 0.28 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.012 0.001 HIS C 101 PHE 0.018 0.001 PHE A 100 TYR 0.020 0.001 TYR D 105 ARG 0.011 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 908) hydrogen bonds : angle 4.67266 ( 2676) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.98073 ( 2) covalent geometry : bond 0.00387 (17066) covalent geometry : angle 0.65233 (23056) ********************** 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 320 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 286 time to evaluate : 1.955 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: 0.9161 (t80) cc_final: 0.8872 (t80) REVERT: A 44 ASN cc_start: 0.9370 (m-40) cc_final: 0.8958 (m-40) REVERT: A 66 GLU cc_start: 0.8672 (tp30) cc_final: 0.8284 (tp30) REVERT: A 110 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.9007 (p0) REVERT: A 217 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8744 (mm-30) REVERT: A 246 SER cc_start: 0.7982 (m) cc_final: 0.7693 (p) REVERT: A 274 ARG cc_start: 0.8119 (ttm110) cc_final: 0.7869 (ttm110) REVERT: A 276 LYS cc_start: 0.9125 (mtpp) cc_final: 0.8874 (mmpt) REVERT: A 286 ASP cc_start: 0.8960 (m-30) cc_final: 0.8190 (m-30) REVERT: A 362 ASP cc_start: 0.8691 (m-30) cc_final: 0.8086 (m-30) REVERT: A 384 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9071 (pp20) REVERT: A 393 SER cc_start: 0.9059 (m) cc_final: 0.8611 (t) REVERT: A 445 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9119 (mm) REVERT: A 452 ARG cc_start: 0.9195 (ttp80) cc_final: 0.8976 (ttp80) REVERT: A 686 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7539 (ptp-110) REVERT: B 104 TYR cc_start: 0.9319 (m-80) cc_final: 0.8563 (m-80) REVERT: B 221 LYS cc_start: 0.9292 (mttm) cc_final: 0.8967 (mttm) REVERT: B 235 ARG cc_start: 0.9042 (ttm-80) cc_final: 0.8820 (ttm-80) REVERT: B 246 SER cc_start: 0.8301 (OUTLIER) cc_final: 0.7738 (p) REVERT: B 274 ARG cc_start: 0.8461 (ttm-80) cc_final: 0.8116 (ttm110) REVERT: B 296 LYS cc_start: 0.8937 (mtpm) cc_final: 0.8732 (mtpp) REVERT: B 348 MET cc_start: 0.9070 (OUTLIER) cc_final: 0.8642 (tmm) REVERT: B 393 SER cc_start: 0.9073 (m) cc_final: 0.8631 (t) REVERT: B 483 GLU cc_start: 0.9042 (mp0) cc_final: 0.8602 (mp0) REVERT: B 570 MET cc_start: 0.9620 (OUTLIER) cc_final: 0.9398 (mtm) REVERT: B 603 GLU cc_start: 0.9072 (tt0) cc_final: 0.8368 (mt-10) REVERT: B 610 LYS cc_start: 0.9031 (ttpp) cc_final: 0.8606 (ttpp) REVERT: B 612 TYR cc_start: 0.8906 (m-80) cc_final: 0.8411 (m-80) REVERT: B 624 PHE cc_start: 0.9249 (m-80) cc_final: 0.8796 (m-80) REVERT: B 686 ARG cc_start: 0.8542 (mtp-110) cc_final: 0.8160 (mtp-110) REVERT: C 85 GLN cc_start: 0.6743 (OUTLIER) cc_final: 0.6256 (tm-30) REVERT: C 96 MET cc_start: 0.7498 (tpt) cc_final: 0.6374 (mpp) REVERT: C 146 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7725 (mm-40) REVERT: D 56 MET cc_start: 0.2483 (ptp) cc_final: 0.2007 (tpt) REVERT: D 74 MET cc_start: 0.2226 (OUTLIER) cc_final: 0.1993 (ptt) REVERT: D 105 TYR cc_start: -0.0872 (OUTLIER) cc_final: -0.1175 (p90) REVERT: E 34 MET cc_start: 0.6379 (mtm) cc_final: 0.6076 (pp-130) outliers start: 34 outliers final: 20 residues processed: 302 average time/residue: 1.3451 time to fit residues: 450.5288 Evaluate side-chains 308 residues out of total 1791 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 279 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 539 LYS Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain C residue 85 GLN Chi-restraints excluded: chain C residue 134 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 241 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 105 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 58 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 191 optimal weight: 9.9990 chunk 167 optimal weight: 30.0000 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 184 optimal weight: 0.3980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.183131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098380 restraints weight = 23373.860| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.86 r_work: 0.2769 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 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 = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17067 Z= 0.182 Angle : 0.649 13.014 23058 Z= 0.327 Chirality : 0.043 0.249 2468 Planarity : 0.003 0.056 2935 Dihedral : 9.929 178.318 2332 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.12 % Allowed : 22.45 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 2016 helix: 1.56 (0.15), residues: 1163 sheet: -0.48 (0.37), residues: 169 loop : 0.34 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 9 HIS 0.009 0.001 HIS C 101 PHE 0.016 0.001 PHE A 100 TYR 0.020 0.001 TYR D 105 ARG 0.010 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 908) hydrogen bonds : angle 4.66595 ( 2676) SS BOND : bond 0.00095 ( 1) SS BOND : angle 0.95520 ( 2) covalent geometry : bond 0.00416 (17066) covalent geometry : angle 0.64937 (23056) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21499.45 seconds wall clock time: 370 minutes 45.31 seconds (22245.31 seconds total)