Starting phenix.real_space_refine on Thu Sep 18 02:02:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duo_47172/09_2025/9duo_47172.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duo_47172/09_2025/9duo_47172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9duo_47172/09_2025/9duo_47172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duo_47172/09_2025/9duo_47172.map" model { file = "/net/cci-nas-00/data/ceres_data/9duo_47172/09_2025/9duo_47172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duo_47172/09_2025/9duo_47172.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 8362 2.51 5 N 2319 2.21 5 O 2408 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13187 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2784 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 15, 'TRANS': 349} Chain breaks: 4 Chain: "B" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2767 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 15, 'TRANS': 347} Chain breaks: 4 Chain: "C" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3821 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 30, 'TRANS': 474} Chain breaks: 7 Chain: "D" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3815 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 29, 'TRANS': 473} Chain breaks: 7 Time building chain proxies: 3.40, per 1000 atoms: 0.26 Number of scatterers: 13187 At special positions: 0 Unit cell: (99.12, 112.336, 114.814, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2408 8.00 N 2319 7.00 C 8362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 712.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3208 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 15 sheets defined 53.1% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 150 through 156 Processing helix chain 'A' and resid 260 through 262 No H-bonds generated for 'chain 'A' and resid 260 through 262' Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 362 through 366 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 150 through 155 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.506A pdb=" N LEU B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 390 Processing helix chain 'C' and resid 30 through 42 removed outlier: 3.657A pdb=" N LEU C 38 " --> pdb=" O ARG C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 89 through 100 removed outlier: 3.524A pdb=" N SER C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 103 No H-bonds generated for 'chain 'C' and resid 101 through 103' Processing helix chain 'C' and resid 104 through 118 removed outlier: 3.538A pdb=" N LEU C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 139 removed outlier: 5.530A pdb=" N VAL C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 163 removed outlier: 3.626A pdb=" N ASP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 191 through 206 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.765A pdb=" N GLY C 211 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N SER C 212 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 removed outlier: 3.591A pdb=" N SER C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ARG C 224 " --> pdb=" O PHE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 256 through 279 Processing helix chain 'C' and resid 306 through 328 removed outlier: 3.539A pdb=" N GLN C 310 " --> pdb=" O HIS C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 351 removed outlier: 4.128A pdb=" N VAL C 351 " --> pdb=" O ARG C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 388 Proline residue: C 370 - end of helix Processing helix chain 'C' and resid 389 through 393 removed outlier: 4.394A pdb=" N ARG C 393 " --> pdb=" O ARG C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 409 removed outlier: 3.670A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'C' and resid 424 through 443 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 451 through 467 removed outlier: 4.015A pdb=" N GLY C 455 " --> pdb=" O GLY C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 537 removed outlier: 3.626A pdb=" N CYS C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 559 Proline residue: C 554 - end of helix Processing helix chain 'C' and resid 568 through 571 Processing helix chain 'C' and resid 572 through 589 Processing helix chain 'C' and resid 597 through 609 Processing helix chain 'C' and resid 613 through 632 Processing helix chain 'D' and resid 30 through 43 removed outlier: 3.906A pdb=" N LEU D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 100 through 103 removed outlier: 6.873A pdb=" N LYS D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 100 through 103' Processing helix chain 'D' and resid 104 through 119 Processing helix chain 'D' and resid 120 through 140 removed outlier: 5.467A pdb=" N VAL D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N SER D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 163 removed outlier: 3.666A pdb=" N ASP D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 207 through 212 removed outlier: 3.595A pdb=" N GLY D 211 " --> pdb=" O ARG D 208 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER D 212 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 223 Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 255 through 279 Processing helix chain 'D' and resid 306 through 328 Processing helix chain 'D' and resid 337 through 350 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 361 through 388 Proline residue: D 370 - end of helix Processing helix chain 'D' and resid 389 through 393 removed outlier: 4.179A pdb=" N ARG D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 409 Proline residue: D 403 - end of helix Processing helix chain 'D' and resid 424 through 443 Processing helix chain 'D' and resid 444 through 446 No H-bonds generated for 'chain 'D' and resid 444 through 446' Processing helix chain 'D' and resid 452 through 466 Processing helix chain 'D' and resid 518 through 537 removed outlier: 3.524A pdb=" N CYS D 522 " --> pdb=" O ASN D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 540 No H-bonds generated for 'chain 'D' and resid 538 through 540' Processing helix chain 'D' and resid 541 through 561 Proline residue: D 554 - end of helix removed outlier: 3.509A pdb=" N MET D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 568 through 571 Processing helix chain 'D' and resid 572 through 589 Processing helix chain 'D' and resid 597 through 609 Processing helix chain 'D' and resid 613 through 632 removed outlier: 3.582A pdb=" N PHE D 619 " --> pdb=" O GLU D 615 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 625 " --> pdb=" O SER D 621 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA D 629 " --> pdb=" O VAL D 625 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.811A pdb=" N VAL A 22 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR A 33 " --> pdb=" O CYS A 20 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N CYS A 20 " --> pdb=" O THR A 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 47 removed outlier: 5.673A pdb=" N GLY A 43 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N TYR A 61 " --> pdb=" O GLN A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 88 removed outlier: 3.683A pdb=" N CYS A 85 " --> pdb=" O GLY A 98 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 115 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLU A 107 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU A 113 " --> pdb=" O GLU A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 124 through 129 removed outlier: 3.500A pdb=" N CYS A 126 " --> pdb=" O GLY A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 180 removed outlier: 3.679A pdb=" N ASP A 177 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N THR A 197 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL A 198 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 211 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU A 200 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ARG A 253 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N SER A 211 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 218 through 223 Processing sheet with id=AA7, first strand: chain 'A' and resid 272 through 277 removed outlier: 4.210A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG A 305 " --> pdb=" O LEU A 295 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP A 297 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N CYS A 303 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 359 Processing sheet with id=AA9, first strand: chain 'B' and resid 30 through 34 removed outlier: 6.655A pdb=" N ASN B 30 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N GLU B 24 " --> pdb=" O ASN B 30 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS B 20 " --> pdb=" O TYR B 34 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASN B 315 " --> pdb=" O THR B 11 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 39 through 47 removed outlier: 5.828A pdb=" N GLY B 43 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TYR B 61 " --> pdb=" O GLN B 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 87 through 88 removed outlier: 3.646A pdb=" N VAL B 115 " --> pdb=" O LEU B 105 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLU B 107 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU B 113 " --> pdb=" O GLU B 107 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 124 through 129 Processing sheet with id=AB4, first strand: chain 'B' and resid 175 through 180 removed outlier: 3.647A pdb=" N ASP B 177 " --> pdb=" O SER B 192 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 197 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLU B 202 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU B 208 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ARG B 253 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER B 211 " --> pdb=" O ARG B 253 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 223 removed outlier: 6.388A pdb=" N GLY B 233 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL B 221 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE B 231 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N MET B 223 " --> pdb=" O HIS B 229 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N HIS B 229 " --> pdb=" O MET B 223 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 272 through 277 removed outlier: 4.154A pdb=" N THR B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP B 297 " --> pdb=" O CYS B 303 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS B 303 " --> pdb=" O ASP B 297 " (cutoff:3.500A) 771 hydrogen bonds defined for protein. 2229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4350 1.34 - 1.46: 2686 1.46 - 1.58: 6265 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 13433 Sorted by residual: bond pdb=" CB LYS C 354 " pdb=" CG LYS C 354 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" CG ASP D 378 " pdb=" OD1 ASP D 378 " ideal model delta sigma weight residual 1.249 1.231 0.018 1.90e-02 2.77e+03 8.66e-01 bond pdb=" CA LEU D 402 " pdb=" C LEU D 402 " ideal model delta sigma weight residual 1.521 1.529 -0.008 1.11e-02 8.12e+03 5.37e-01 bond pdb=" CB THR A 33 " pdb=" CG2 THR A 33 " ideal model delta sigma weight residual 1.521 1.498 0.023 3.30e-02 9.18e+02 5.02e-01 bond pdb=" C ILE D 398 " pdb=" O ILE D 398 " ideal model delta sigma weight residual 1.237 1.245 -0.008 1.19e-02 7.06e+03 4.86e-01 ... (remaining 13428 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 17943 1.54 - 3.07: 216 3.07 - 4.61: 40 4.61 - 6.15: 12 6.15 - 7.68: 1 Bond angle restraints: 18212 Sorted by residual: angle pdb=" N ARG A 119 " pdb=" CA ARG A 119 " pdb=" C ARG A 119 " ideal model delta sigma weight residual 114.04 109.79 4.25 1.24e+00 6.50e-01 1.18e+01 angle pdb=" CA LYS C 354 " pdb=" CB LYS C 354 " pdb=" CG LYS C 354 " ideal model delta sigma weight residual 114.10 119.32 -5.22 2.00e+00 2.50e-01 6.81e+00 angle pdb=" N ASP D 378 " pdb=" CA ASP D 378 " pdb=" CB ASP D 378 " ideal model delta sigma weight residual 110.28 113.95 -3.67 1.55e+00 4.16e-01 5.61e+00 angle pdb=" CA LEU D 38 " pdb=" CB LEU D 38 " pdb=" CG LEU D 38 " ideal model delta sigma weight residual 116.30 123.98 -7.68 3.50e+00 8.16e-02 4.82e+00 angle pdb=" N GLY C 537 " pdb=" CA GLY C 537 " pdb=" C GLY C 537 " ideal model delta sigma weight residual 112.34 116.50 -4.16 2.04e+00 2.40e-01 4.16e+00 ... (remaining 18207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 6942 17.81 - 35.62: 855 35.62 - 53.42: 225 53.42 - 71.23: 65 71.23 - 89.04: 20 Dihedral angle restraints: 8107 sinusoidal: 3161 harmonic: 4946 Sorted by residual: dihedral pdb=" CA ASP D 514 " pdb=" CB ASP D 514 " pdb=" CG ASP D 514 " pdb=" OD1 ASP D 514 " ideal model delta sinusoidal sigma weight residual -30.00 -89.01 59.01 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA TYR D 570 " pdb=" C TYR D 570 " pdb=" N THR D 571 " pdb=" CA THR D 571 " ideal model delta harmonic sigma weight residual 180.00 163.06 16.94 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA TYR C 570 " pdb=" C TYR C 570 " pdb=" N THR C 571 " pdb=" CA THR C 571 " ideal model delta harmonic sigma weight residual 180.00 163.11 16.89 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 8104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1482 0.032 - 0.064: 462 0.064 - 0.096: 119 0.096 - 0.128: 88 0.128 - 0.160: 5 Chirality restraints: 2156 Sorted by residual: chirality pdb=" CG LEU D 38 " pdb=" CB LEU D 38 " pdb=" CD1 LEU D 38 " pdb=" CD2 LEU D 38 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.40e-01 chirality pdb=" CA ILE B 318 " pdb=" N ILE B 318 " pdb=" C ILE B 318 " pdb=" CB ILE B 318 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.66e-01 chirality pdb=" CA ILE B 116 " pdb=" N ILE B 116 " pdb=" C ILE B 116 " pdb=" CB ILE B 116 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 2153 not shown) Planarity restraints: 2301 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY B 184 " -0.045 5.00e-02 4.00e+02 6.84e-02 7.50e+00 pdb=" N PRO B 185 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 362 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00 pdb=" N PRO C 363 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 363 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 363 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 362 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 363 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 363 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 363 " 0.024 5.00e-02 4.00e+02 ... (remaining 2298 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 569 2.73 - 3.27: 12325 3.27 - 3.81: 22826 3.81 - 4.36: 28826 4.36 - 4.90: 48792 Nonbonded interactions: 113338 Sorted by model distance: nonbonded pdb=" OG SER B 89 " pdb=" OG SER B 133 " model vdw 2.186 3.040 nonbonded pdb=" OH TYR C 432 " pdb=" OD2 ASP C 465 " model vdw 2.200 3.040 nonbonded pdb=" O LEU D 614 " pdb=" OG SER D 618 " model vdw 2.209 3.040 nonbonded pdb=" O LEU C 115 " pdb=" OG SER C 119 " model vdw 2.220 3.040 nonbonded pdb=" O ASP D 143 " pdb=" NH2 ARG D 188 " model vdw 2.220 3.120 ... (remaining 113333 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 5 through 156 or resid 161 through 255 or resid 261 throug \ h 390)) selection = (chain 'B' and (resid 5 through 245 or resid 251 through 390)) } ncs_group { reference = (chain 'C' and (resid 29 through 80 or resid 88 through 280 or resid 305 through \ 469 or resid 511 through 635)) selection = (chain 'D' and (resid 29 through 80 or resid 88 through 247 or resid 255 through \ 469 or resid 511 through 635)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 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 : 0.002 0.031 13433 Z= 0.102 Angle : 0.480 7.685 18212 Z= 0.245 Chirality : 0.038 0.160 2156 Planarity : 0.004 0.068 2301 Dihedral : 17.776 89.040 4899 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.20 % Allowed : 22.11 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.20), residues: 1684 helix: 1.96 (0.18), residues: 820 sheet: 0.40 (0.33), residues: 257 loop : 0.40 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.010 0.001 TYR B 94 PHE 0.014 0.001 PHE B 136 TRP 0.011 0.001 TRP A 148 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00227 (13433) covalent geometry : angle 0.48047 (18212) hydrogen bonds : bond 0.16318 ( 771) hydrogen bonds : angle 5.96878 ( 2229) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.545 Fit side-chains REVERT: A 236 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.6801 (pp20) REVERT: A 299 GLN cc_start: 0.7885 (mm-40) cc_final: 0.6949 (tm-30) REVERT: A 369 GLU cc_start: 0.7011 (mp0) cc_final: 0.6207 (pm20) REVERT: B 46 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8644 (tt) REVERT: B 57 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8281 (tt) REVERT: B 72 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: B 263 LYS cc_start: 0.8221 (mttm) cc_final: 0.7825 (mtmt) REVERT: B 365 GLN cc_start: 0.7742 (pt0) cc_final: 0.7284 (pp30) REVERT: B 369 GLU cc_start: 0.5863 (OUTLIER) cc_final: 0.4843 (mp0) REVERT: B 387 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6168 (tmm) REVERT: C 98 ARG cc_start: 0.7776 (mmt-90) cc_final: 0.7469 (mmt90) REVERT: C 118 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 170 ARG cc_start: 0.6612 (tpm170) cc_final: 0.6040 (mtt90) REVERT: C 190 GLU cc_start: 0.7809 (mp0) cc_final: 0.7430 (pm20) REVERT: C 208 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7150 (ttp-170) REVERT: C 312 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7340 (ttp80) REVERT: C 320 ARG cc_start: 0.7973 (ttm110) cc_final: 0.7643 (tpp80) REVERT: C 361 ASP cc_start: 0.7774 (t0) cc_final: 0.7336 (t0) REVERT: C 420 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.6825 (mm-40) REVERT: C 527 ARG cc_start: 0.8412 (mtp180) cc_final: 0.7647 (mtt90) REVERT: C 574 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7649 (ttp-110) REVERT: D 216 LYS cc_start: 0.8577 (mtpp) cc_final: 0.8340 (mttp) REVERT: D 314 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7359 (ttp-170) REVERT: D 389 SER cc_start: 0.8215 (p) cc_final: 0.7949 (t) REVERT: D 420 GLN cc_start: 0.7456 (tt0) cc_final: 0.7112 (tm-30) REVERT: D 511 ARG cc_start: 0.6868 (mmm160) cc_final: 0.6603 (mtp85) REVERT: D 529 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8219 (tt) REVERT: D 541 LYS cc_start: 0.8590 (ptpt) cc_final: 0.8337 (pttt) REVERT: D 543 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7983 (mp0) outliers start: 47 outliers final: 28 residues processed: 214 average time/residue: 0.7711 time to fit residues: 176.6573 Evaluate side-chains 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 529 LEU Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 611 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.102891 restraints weight = 12988.385| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.38 r_work: 0.3020 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13433 Z= 0.207 Angle : 0.629 7.971 18212 Z= 0.321 Chirality : 0.045 0.153 2156 Planarity : 0.006 0.068 2301 Dihedral : 8.511 87.893 1921 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.37 % Allowed : 20.07 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.20), residues: 1684 helix: 1.91 (0.18), residues: 831 sheet: 0.21 (0.31), residues: 277 loop : 0.38 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 188 TYR 0.014 0.002 TYR D 205 PHE 0.020 0.002 PHE C 619 TRP 0.020 0.002 TRP B 201 HIS 0.006 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00497 (13433) covalent geometry : angle 0.62859 (18212) hydrogen bonds : bond 0.05543 ( 771) hydrogen bonds : angle 4.87637 ( 2229) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 172 time to evaluate : 0.483 Fit side-chains REVERT: A 236 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.6975 (pp20) REVERT: A 299 GLN cc_start: 0.7860 (mm-40) cc_final: 0.6879 (tm-30) REVERT: B 75 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: B 263 LYS cc_start: 0.8209 (mttm) cc_final: 0.7805 (mtmt) REVERT: B 369 GLU cc_start: 0.5842 (OUTLIER) cc_final: 0.4886 (tt0) REVERT: B 387 MET cc_start: 0.6845 (OUTLIER) cc_final: 0.6241 (tmm) REVERT: C 98 ARG cc_start: 0.7649 (mmt-90) cc_final: 0.7339 (mmt90) REVERT: C 118 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: C 170 ARG cc_start: 0.6612 (tpm170) cc_final: 0.5931 (mtt90) REVERT: C 208 ARG cc_start: 0.8079 (ttt180) cc_final: 0.6974 (tmm160) REVERT: C 312 ARG cc_start: 0.7992 (ttp-170) cc_final: 0.7349 (ttp80) REVERT: C 320 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7651 (tpp80) REVERT: C 420 GLN cc_start: 0.7419 (OUTLIER) cc_final: 0.6686 (mm-40) REVERT: C 527 ARG cc_start: 0.8460 (mtp180) cc_final: 0.7608 (mtt90) REVERT: C 557 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8140 (mtp) REVERT: C 574 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7817 (ttp-110) REVERT: D 216 LYS cc_start: 0.8493 (mtpp) cc_final: 0.7820 (mtmm) REVERT: D 314 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7130 (ttm110) REVERT: D 325 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8606 (mtm) REVERT: D 420 GLN cc_start: 0.7412 (tt0) cc_final: 0.7052 (tm-30) REVERT: D 543 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8012 (mp0) outliers start: 79 outliers final: 36 residues processed: 227 average time/residue: 0.7010 time to fit residues: 171.2733 Evaluate side-chains 213 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 162 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 146 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 157 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 380 GLN B 72 GLN B 75 GLN D 407 ASN D 603 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.123014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.099352 restraints weight = 13362.548| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.35 r_work: 0.2966 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13433 Z= 0.255 Angle : 0.687 8.428 18212 Z= 0.348 Chirality : 0.048 0.155 2156 Planarity : 0.006 0.071 2301 Dihedral : 7.781 89.593 1882 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 6.12 % Allowed : 18.98 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.20), residues: 1684 helix: 1.69 (0.17), residues: 833 sheet: 0.16 (0.31), residues: 265 loop : 0.16 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 188 TYR 0.017 0.002 TYR D 205 PHE 0.023 0.003 PHE C 619 TRP 0.021 0.003 TRP A 201 HIS 0.006 0.001 HIS C 265 Details of bonding type rmsd covalent geometry : bond 0.00625 (13433) covalent geometry : angle 0.68692 (18212) hydrogen bonds : bond 0.05886 ( 771) hydrogen bonds : angle 4.91820 ( 2229) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 168 time to evaluate : 0.547 Fit side-chains REVERT: A 236 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: A 299 GLN cc_start: 0.7891 (mm-40) cc_final: 0.6962 (tm-30) REVERT: B 5 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.6916 (tpp) REVERT: B 263 LYS cc_start: 0.8197 (mttm) cc_final: 0.7816 (mtmt) REVERT: B 369 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.4915 (tt0) REVERT: B 387 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6195 (tmm) REVERT: C 98 ARG cc_start: 0.7740 (mmt-90) cc_final: 0.7428 (mmt90) REVERT: C 118 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: C 170 ARG cc_start: 0.6768 (tpm170) cc_final: 0.6130 (mtt90) REVERT: C 208 ARG cc_start: 0.8090 (ttt180) cc_final: 0.7021 (tmm160) REVERT: C 312 ARG cc_start: 0.8085 (ttp-170) cc_final: 0.7452 (ttp80) REVERT: C 320 ARG cc_start: 0.7954 (ttm170) cc_final: 0.7694 (tpp80) REVERT: C 420 GLN cc_start: 0.7388 (OUTLIER) cc_final: 0.6629 (mm-40) REVERT: C 527 ARG cc_start: 0.8475 (mtp180) cc_final: 0.7679 (mtt90) REVERT: C 557 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: C 574 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7776 (ttp-110) REVERT: D 216 LYS cc_start: 0.8554 (mtpp) cc_final: 0.7902 (mtmm) REVERT: D 314 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7212 (ttm110) REVERT: D 420 GLN cc_start: 0.7493 (tt0) cc_final: 0.7148 (tm-30) REVERT: D 511 ARG cc_start: 0.6936 (mmm160) cc_final: 0.6695 (mtp85) outliers start: 90 outliers final: 49 residues processed: 227 average time/residue: 0.7106 time to fit residues: 173.8625 Evaluate side-chains 224 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 166 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 236 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 329 GLU Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 153 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 140 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 31 optimal weight: 0.0270 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 162 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN C 262 GLN D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.106247 restraints weight = 13114.819| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.36 r_work: 0.3058 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13433 Z= 0.119 Angle : 0.519 6.262 18212 Z= 0.268 Chirality : 0.040 0.148 2156 Planarity : 0.005 0.069 2301 Dihedral : 6.974 87.437 1876 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 4.56 % Allowed : 20.54 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.20), residues: 1684 helix: 2.19 (0.18), residues: 834 sheet: 0.21 (0.31), residues: 267 loop : 0.27 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 188 TYR 0.012 0.002 TYR D 205 PHE 0.015 0.002 PHE B 136 TRP 0.019 0.002 TRP A 148 HIS 0.003 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00273 (13433) covalent geometry : angle 0.51881 (18212) hydrogen bonds : bond 0.04219 ( 771) hydrogen bonds : angle 4.48830 ( 2229) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 174 time to evaluate : 0.543 Fit side-chains REVERT: A 74 GLN cc_start: 0.7420 (OUTLIER) cc_final: 0.7051 (mp-120) REVERT: A 75 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: A 141 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8698 (mttt) REVERT: A 299 GLN cc_start: 0.7852 (mm-40) cc_final: 0.6879 (tm-30) REVERT: B 13 SER cc_start: 0.8351 (t) cc_final: 0.8136 (p) REVERT: B 102 SER cc_start: 0.8894 (OUTLIER) cc_final: 0.8559 (m) REVERT: B 263 LYS cc_start: 0.8138 (mttm) cc_final: 0.7787 (mtmt) REVERT: B 369 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.4702 (mp0) REVERT: B 387 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6134 (tmm) REVERT: C 98 ARG cc_start: 0.7660 (mmt-90) cc_final: 0.7350 (mmt90) REVERT: C 118 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: C 119 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7824 (m) REVERT: C 170 ARG cc_start: 0.6640 (tpm170) cc_final: 0.6016 (mtt90) REVERT: C 208 ARG cc_start: 0.8036 (ttt180) cc_final: 0.6920 (tmm160) REVERT: C 311 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8015 (mp) REVERT: C 312 ARG cc_start: 0.8034 (ttp-170) cc_final: 0.7306 (ttp80) REVERT: C 320 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7654 (tpp80) REVERT: C 420 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.6653 (mm-40) REVERT: C 527 ARG cc_start: 0.8389 (mtp180) cc_final: 0.7603 (mtt90) REVERT: C 535 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7815 (mmp) REVERT: C 557 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8083 (mtp) REVERT: D 119 SER cc_start: 0.8026 (OUTLIER) cc_final: 0.7585 (p) REVERT: D 216 LYS cc_start: 0.8446 (mtpp) cc_final: 0.7791 (mtmm) REVERT: D 314 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7114 (ttm110) REVERT: D 420 GLN cc_start: 0.7427 (tt0) cc_final: 0.7077 (tm-30) REVERT: D 511 ARG cc_start: 0.6907 (mmm160) cc_final: 0.6682 (mtp85) REVERT: D 529 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8133 (tt) REVERT: D 543 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.8030 (mp0) outliers start: 67 outliers final: 33 residues processed: 219 average time/residue: 0.7409 time to fit residues: 174.2062 Evaluate side-chains 217 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 168 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 84 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 115 optimal weight: 0.0170 chunk 47 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 171 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 378 GLN B 75 GLN C 233 GLN D 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.105041 restraints weight = 13188.503| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.36 r_work: 0.3054 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13433 Z= 0.149 Angle : 0.554 6.589 18212 Z= 0.284 Chirality : 0.042 0.147 2156 Planarity : 0.005 0.065 2301 Dihedral : 6.641 87.487 1865 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 5.24 % Allowed : 19.80 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.20), residues: 1684 helix: 2.19 (0.17), residues: 839 sheet: 0.14 (0.31), residues: 267 loop : 0.28 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 188 TYR 0.016 0.002 TYR D 205 PHE 0.018 0.002 PHE C 619 TRP 0.017 0.002 TRP A 201 HIS 0.004 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00351 (13433) covalent geometry : angle 0.55424 (18212) hydrogen bonds : bond 0.04552 ( 771) hydrogen bonds : angle 4.50858 ( 2229) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 170 time to evaluate : 0.557 Fit side-chains REVERT: A 74 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.6725 (mp-120) REVERT: A 299 GLN cc_start: 0.7876 (mm-40) cc_final: 0.6925 (tm-30) REVERT: B 13 SER cc_start: 0.8378 (t) cc_final: 0.8154 (p) REVERT: B 75 GLN cc_start: 0.7214 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: B 78 MET cc_start: 0.8681 (mmm) cc_final: 0.8399 (mmt) REVERT: B 263 LYS cc_start: 0.8155 (mttm) cc_final: 0.7815 (mtmt) REVERT: B 369 GLU cc_start: 0.5876 (OUTLIER) cc_final: 0.4712 (mp0) REVERT: B 387 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.6078 (tmm) REVERT: C 98 ARG cc_start: 0.7671 (mmt-90) cc_final: 0.7357 (mmt90) REVERT: C 118 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: C 170 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6076 (mtt90) REVERT: C 208 ARG cc_start: 0.8076 (ttt180) cc_final: 0.6959 (tmm160) REVERT: C 311 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8018 (mp) REVERT: C 312 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7310 (ttp80) REVERT: C 320 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7657 (tpp80) REVERT: C 420 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.6666 (mm-40) REVERT: C 527 ARG cc_start: 0.8385 (mtp180) cc_final: 0.7601 (mtt90) REVERT: C 535 MET cc_start: 0.8801 (OUTLIER) cc_final: 0.7815 (mmp) REVERT: C 557 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (mtp) REVERT: D 119 SER cc_start: 0.8088 (OUTLIER) cc_final: 0.7618 (p) REVERT: D 216 LYS cc_start: 0.8469 (mtpp) cc_final: 0.7815 (mtmm) REVERT: D 314 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7149 (ttm110) REVERT: D 420 GLN cc_start: 0.7441 (tt0) cc_final: 0.7088 (tm-30) REVERT: D 529 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8173 (tt) REVERT: D 543 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7067 (mm-30) outliers start: 77 outliers final: 41 residues processed: 219 average time/residue: 0.7174 time to fit residues: 168.8977 Evaluate side-chains 223 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 74 GLN Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.125771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.102361 restraints weight = 13138.591| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 1.36 r_work: 0.3006 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 13433 Z= 0.256 Angle : 0.679 9.054 18212 Z= 0.343 Chirality : 0.048 0.259 2156 Planarity : 0.006 0.068 2301 Dihedral : 7.094 89.356 1865 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 5.92 % Allowed : 18.98 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.20), residues: 1684 helix: 1.81 (0.17), residues: 836 sheet: 0.10 (0.31), residues: 267 loop : 0.21 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.019 0.002 TYR D 205 PHE 0.024 0.003 PHE D 619 TRP 0.019 0.003 TRP A 201 HIS 0.006 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00626 (13433) covalent geometry : angle 0.67892 (18212) hydrogen bonds : bond 0.05687 ( 771) hydrogen bonds : angle 4.80102 ( 2229) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 170 time to evaluate : 0.525 Fit side-chains REVERT: A 69 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.6963 (mtp85) REVERT: A 74 GLN cc_start: 0.7265 (tp40) cc_final: 0.6875 (mp-120) REVERT: A 141 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8729 (mttt) REVERT: A 299 GLN cc_start: 0.7838 (mm-40) cc_final: 0.6868 (tm-30) REVERT: B 5 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.6947 (tpp) REVERT: B 35 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7451 (ttm-80) REVERT: B 263 LYS cc_start: 0.8195 (mttm) cc_final: 0.7825 (mtmt) REVERT: B 369 GLU cc_start: 0.5928 (OUTLIER) cc_final: 0.4890 (tt0) REVERT: B 387 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6072 (tmm) REVERT: C 98 ARG cc_start: 0.7691 (mmt-90) cc_final: 0.7380 (mmt90) REVERT: C 118 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: C 170 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.6123 (mtt90) REVERT: C 208 ARG cc_start: 0.8124 (ttt180) cc_final: 0.6986 (tmm160) REVERT: C 312 ARG cc_start: 0.8108 (ttp-170) cc_final: 0.7412 (ttp80) REVERT: C 320 ARG cc_start: 0.7925 (ttm170) cc_final: 0.7666 (tpp80) REVERT: C 420 GLN cc_start: 0.7341 (OUTLIER) cc_final: 0.6569 (mm-40) REVERT: C 527 ARG cc_start: 0.8435 (mtp180) cc_final: 0.7659 (mtt90) REVERT: C 557 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8184 (mtp) REVERT: C 574 ARG cc_start: 0.8167 (ttp-170) cc_final: 0.7829 (ttp-110) REVERT: D 216 LYS cc_start: 0.8546 (mtpp) cc_final: 0.7877 (mtmm) REVERT: D 314 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7169 (ttm110) REVERT: D 420 GLN cc_start: 0.7468 (tt0) cc_final: 0.7112 (tm-30) outliers start: 87 outliers final: 54 residues processed: 228 average time/residue: 0.7124 time to fit residues: 175.1506 Evaluate side-chains 229 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 164 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 5 MET Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 556 VAL Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 155 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN C 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.104743 restraints weight = 13072.017| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.35 r_work: 0.3049 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13433 Z= 0.146 Angle : 0.559 7.583 18212 Z= 0.286 Chirality : 0.042 0.172 2156 Planarity : 0.005 0.070 2301 Dihedral : 6.757 88.403 1865 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.63 % Allowed : 20.07 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.20), residues: 1684 helix: 2.07 (0.17), residues: 841 sheet: 0.14 (0.31), residues: 267 loop : 0.26 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.015 0.002 TYR D 205 PHE 0.018 0.002 PHE C 619 TRP 0.018 0.002 TRP A 201 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00344 (13433) covalent geometry : angle 0.55873 (18212) hydrogen bonds : bond 0.04577 ( 771) hydrogen bonds : angle 4.55627 ( 2229) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 177 time to evaluate : 0.524 Fit side-chains REVERT: A 74 GLN cc_start: 0.7472 (tp40) cc_final: 0.6960 (mp-120) REVERT: A 141 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8677 (mttt) REVERT: A 299 GLN cc_start: 0.7854 (mm-40) cc_final: 0.6900 (tm-30) REVERT: B 13 SER cc_start: 0.8402 (t) cc_final: 0.8178 (p) REVERT: B 35 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7667 (ttm-80) REVERT: B 57 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8345 (tt) REVERT: B 263 LYS cc_start: 0.8153 (mttm) cc_final: 0.7742 (mtmt) REVERT: B 369 GLU cc_start: 0.5967 (OUTLIER) cc_final: 0.4988 (tt0) REVERT: B 387 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6056 (tmm) REVERT: C 98 ARG cc_start: 0.7693 (mmt-90) cc_final: 0.7382 (mmt90) REVERT: C 118 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7169 (mt-10) REVERT: C 170 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6131 (mtt90) REVERT: C 208 ARG cc_start: 0.8092 (ttt180) cc_final: 0.6944 (tmm160) REVERT: C 213 LEU cc_start: 0.8157 (mp) cc_final: 0.7810 (mt) REVERT: C 311 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8066 (mp) REVERT: C 312 ARG cc_start: 0.8127 (ttp-170) cc_final: 0.7384 (ttp80) REVERT: C 320 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7666 (tpp80) REVERT: C 420 GLN cc_start: 0.7440 (OUTLIER) cc_final: 0.6657 (mm-40) REVERT: C 527 ARG cc_start: 0.8377 (mtp180) cc_final: 0.7603 (mtt90) REVERT: C 535 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.7832 (mmp) REVERT: C 557 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8093 (mtp) REVERT: C 574 ARG cc_start: 0.8145 (ttp-170) cc_final: 0.7809 (ttp-110) REVERT: D 216 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8303 (mttp) REVERT: D 314 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7176 (ttm110) REVERT: D 420 GLN cc_start: 0.7471 (tt0) cc_final: 0.7145 (tm-30) outliers start: 68 outliers final: 44 residues processed: 220 average time/residue: 0.7661 time to fit residues: 180.7968 Evaluate side-chains 229 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 173 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 145 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN C 262 GLN D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.126777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.103437 restraints weight = 13054.377| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.35 r_work: 0.3020 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13433 Z= 0.200 Angle : 0.619 7.836 18212 Z= 0.314 Chirality : 0.045 0.179 2156 Planarity : 0.006 0.067 2301 Dihedral : 6.932 88.973 1865 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 5.03 % Allowed : 20.07 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.54 (0.20), residues: 1684 helix: 1.94 (0.17), residues: 840 sheet: 0.11 (0.31), residues: 267 loop : 0.23 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 546 TYR 0.019 0.002 TYR D 205 PHE 0.022 0.002 PHE C 619 TRP 0.019 0.002 TRP A 201 HIS 0.005 0.001 HIS D 265 Details of bonding type rmsd covalent geometry : bond 0.00486 (13433) covalent geometry : angle 0.61897 (18212) hydrogen bonds : bond 0.05136 ( 771) hydrogen bonds : angle 4.67651 ( 2229) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 172 time to evaluate : 0.649 Fit side-chains REVERT: A 74 GLN cc_start: 0.7378 (tp40) cc_final: 0.6982 (mp-120) REVERT: A 141 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8707 (mttt) REVERT: A 299 GLN cc_start: 0.7856 (mm-40) cc_final: 0.6872 (tm-30) REVERT: B 35 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7491 (ttm-80) REVERT: B 57 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8321 (tt) REVERT: B 263 LYS cc_start: 0.8179 (mttm) cc_final: 0.7815 (mtmt) REVERT: B 369 GLU cc_start: 0.5871 (OUTLIER) cc_final: 0.4878 (tt0) REVERT: B 387 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6046 (tmm) REVERT: C 98 ARG cc_start: 0.7678 (mmt-90) cc_final: 0.7365 (mmt90) REVERT: C 118 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7224 (mt-10) REVERT: C 170 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6117 (mtt90) REVERT: C 208 ARG cc_start: 0.8128 (ttt180) cc_final: 0.6990 (tmm160) REVERT: C 312 ARG cc_start: 0.8109 (ttp-170) cc_final: 0.7346 (ttp80) REVERT: C 320 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7645 (tpp80) REVERT: C 420 GLN cc_start: 0.7403 (OUTLIER) cc_final: 0.6619 (mm-40) REVERT: C 527 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7631 (mtt90) REVERT: C 557 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: C 574 ARG cc_start: 0.8183 (ttp-170) cc_final: 0.7863 (ttp-110) REVERT: D 216 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8298 (mttp) REVERT: D 314 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7137 (ttm110) REVERT: D 420 GLN cc_start: 0.7460 (tt0) cc_final: 0.7110 (tm-30) outliers start: 74 outliers final: 50 residues processed: 220 average time/residue: 0.7321 time to fit residues: 173.3347 Evaluate side-chains 230 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 366 GLN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 78 SER Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 150 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 91 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN C 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.128187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.104898 restraints weight = 13124.249| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.35 r_work: 0.3041 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13433 Z= 0.142 Angle : 0.555 7.296 18212 Z= 0.285 Chirality : 0.042 0.155 2156 Planarity : 0.005 0.070 2301 Dihedral : 6.708 88.190 1865 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.56 % Allowed : 20.61 % Favored : 74.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.20), residues: 1684 helix: 2.15 (0.17), residues: 841 sheet: 0.13 (0.31), residues: 267 loop : 0.28 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.017 0.002 TYR D 205 PHE 0.017 0.002 PHE C 619 TRP 0.018 0.002 TRP A 201 HIS 0.004 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00334 (13433) covalent geometry : angle 0.55460 (18212) hydrogen bonds : bond 0.04514 ( 771) hydrogen bonds : angle 4.52615 ( 2229) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 172 time to evaluate : 0.537 Fit side-chains REVERT: A 74 GLN cc_start: 0.7486 (tp40) cc_final: 0.6941 (mp-120) REVERT: A 75 GLN cc_start: 0.6350 (OUTLIER) cc_final: 0.6113 (tt0) REVERT: A 141 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8678 (mttt) REVERT: A 299 GLN cc_start: 0.7849 (mm-40) cc_final: 0.6873 (tm-30) REVERT: B 13 SER cc_start: 0.8410 (t) cc_final: 0.8165 (p) REVERT: B 35 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7620 (ttm-80) REVERT: B 57 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8341 (tt) REVERT: B 263 LYS cc_start: 0.8181 (mttm) cc_final: 0.7770 (mtmt) REVERT: B 369 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.4939 (tt0) REVERT: B 387 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.5994 (tmm) REVERT: C 98 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7355 (mmt90) REVERT: C 118 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7227 (mt-10) REVERT: C 170 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.6124 (mtt90) REVERT: C 208 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7148 (ttp-110) REVERT: C 213 LEU cc_start: 0.8175 (mp) cc_final: 0.7823 (mt) REVERT: C 311 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8036 (mp) REVERT: C 312 ARG cc_start: 0.8134 (ttp-170) cc_final: 0.7375 (ttp80) REVERT: C 314 ARG cc_start: 0.7949 (tpt170) cc_final: 0.6896 (ttt180) REVERT: C 320 ARG cc_start: 0.7940 (ttm170) cc_final: 0.7651 (tpp80) REVERT: C 420 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6658 (mm-40) REVERT: C 527 ARG cc_start: 0.8383 (mtp180) cc_final: 0.7583 (mtt90) REVERT: C 535 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.7815 (mmp) REVERT: C 557 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8077 (mtp) REVERT: C 574 ARG cc_start: 0.8139 (ttp-170) cc_final: 0.7774 (ttp-110) REVERT: D 216 LYS cc_start: 0.8516 (mtpp) cc_final: 0.8296 (mttp) REVERT: D 314 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7123 (ttm110) REVERT: D 420 GLN cc_start: 0.7444 (tt0) cc_final: 0.7182 (tm-30) outliers start: 67 outliers final: 44 residues processed: 215 average time/residue: 0.7653 time to fit residues: 176.9585 Evaluate side-chains 225 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 75 GLN Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 51 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.127650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104301 restraints weight = 13148.057| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.36 r_work: 0.3033 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13433 Z= 0.167 Angle : 0.582 7.435 18212 Z= 0.298 Chirality : 0.043 0.158 2156 Planarity : 0.005 0.067 2301 Dihedral : 6.742 88.248 1865 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.29 % Allowed : 20.82 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.20), residues: 1684 helix: 2.08 (0.17), residues: 841 sheet: 0.11 (0.31), residues: 267 loop : 0.29 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.017 0.002 TYR D 205 PHE 0.019 0.002 PHE C 619 TRP 0.018 0.002 TRP A 201 HIS 0.004 0.001 HIS C 545 Details of bonding type rmsd covalent geometry : bond 0.00400 (13433) covalent geometry : angle 0.58153 (18212) hydrogen bonds : bond 0.04745 ( 771) hydrogen bonds : angle 4.57251 ( 2229) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3368 Ramachandran restraints generated. 1684 Oldfield, 0 Emsley, 1684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 169 time to evaluate : 0.562 Fit side-chains REVERT: A 74 GLN cc_start: 0.7341 (tp40) cc_final: 0.6838 (mp-120) REVERT: A 141 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8674 (mttt) REVERT: A 299 GLN cc_start: 0.7840 (mm-40) cc_final: 0.6881 (tm-30) REVERT: B 13 SER cc_start: 0.8401 (t) cc_final: 0.8148 (p) REVERT: B 35 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.7533 (ttm-80) REVERT: B 57 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8324 (tt) REVERT: B 263 LYS cc_start: 0.8182 (mttm) cc_final: 0.7774 (mtmt) REVERT: B 369 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.4934 (tt0) REVERT: B 387 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.5996 (tmm) REVERT: C 98 ARG cc_start: 0.7664 (mmt-90) cc_final: 0.7352 (mmt90) REVERT: C 118 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7256 (mt-10) REVERT: C 170 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6121 (mtt90) REVERT: C 208 ARG cc_start: 0.8122 (ttt180) cc_final: 0.7168 (ttp-110) REVERT: C 311 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8014 (mp) REVERT: C 312 ARG cc_start: 0.8150 (ttp-170) cc_final: 0.7381 (ttp80) REVERT: C 320 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7641 (tpp80) REVERT: C 420 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6662 (mm-40) REVERT: C 527 ARG cc_start: 0.8390 (mtp180) cc_final: 0.7585 (mtt90) REVERT: C 535 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7840 (mmp) REVERT: C 557 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8076 (mtp) REVERT: C 574 ARG cc_start: 0.8151 (ttp-170) cc_final: 0.7787 (ttp-110) REVERT: D 216 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8292 (mttp) REVERT: D 314 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7135 (ttm110) REVERT: D 420 GLN cc_start: 0.7464 (tt0) cc_final: 0.7125 (tm-30) REVERT: D 529 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8156 (tt) outliers start: 63 outliers final: 46 residues processed: 212 average time/residue: 0.7758 time to fit residues: 176.6241 Evaluate side-chains 226 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 167 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 266 LYS Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 378 GLN Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain C residue 34 ARG Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 118 GLU Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain C residue 143 ASP Chi-restraints excluded: chain C residue 170 ARG Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 351 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 381 SER Chi-restraints excluded: chain C residue 420 GLN Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 535 MET Chi-restraints excluded: chain C residue 557 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 130 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 212 SER Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 371 SER Chi-restraints excluded: chain D residue 389 SER Chi-restraints excluded: chain D residue 425 SER Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 529 LEU Chi-restraints excluded: chain D residue 543 GLU Chi-restraints excluded: chain D residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 151 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 102 optimal weight: 0.8980 chunk 26 optimal weight: 0.0670 chunk 112 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN C 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.131049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.108946 restraints weight = 12990.769| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.27 r_work: 0.3075 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13433 Z= 0.102 Angle : 0.497 6.700 18212 Z= 0.257 Chirality : 0.039 0.142 2156 Planarity : 0.005 0.069 2301 Dihedral : 6.263 86.029 1865 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.13 % Allowed : 22.11 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.20), residues: 1684 helix: 2.44 (0.18), residues: 840 sheet: 0.16 (0.31), residues: 269 loop : 0.41 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 34 TYR 0.013 0.001 TYR D 205 PHE 0.014 0.001 PHE B 136 TRP 0.020 0.002 TRP A 148 HIS 0.005 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00222 (13433) covalent geometry : angle 0.49716 (18212) hydrogen bonds : bond 0.03769 ( 771) hydrogen bonds : angle 4.30247 ( 2229) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5062.45 seconds wall clock time: 87 minutes 4.39 seconds (5224.39 seconds total)