Starting phenix.real_space_refine on Wed Jun 11 19:25:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9duo_47172/06_2025/9duo_47172.cif Found real_map, /net/cci-nas-00/data/ceres_data/9duo_47172/06_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_47172/06_2025/9duo_47172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9duo_47172/06_2025/9duo_47172.map" model { file = "/net/cci-nas-00/data/ceres_data/9duo_47172/06_2025/9duo_47172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9duo_47172/06_2025/9duo_47172.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.058 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.69, per 1000 atoms: 0.66 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: 3.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.48 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: 4.38 Time building geometry restraints manager: 3.65 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: 3.110 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 32.610 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.390 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.20), 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 TRP 0.011 0.001 TRP A 148 HIS 0.004 0.001 HIS A 120 PHE 0.014 0.001 PHE B 136 TYR 0.010 0.001 TYR B 94 ARG 0.003 0.000 ARG D 34 Details of bonding type rmsd hydrogen bonds : bond 0.16318 ( 771) hydrogen bonds : angle 5.96878 ( 2229) covalent geometry : bond 0.00227 (13433) covalent geometry : angle 0.48047 (18212) *********************** 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 : 1.404 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: 1.5193 time to fit residues: 349.3491 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 : 1.517 ------------------------------------------------------------------------------- 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 145 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 72 GLN B 75 GLN D 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.122303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.098767 restraints weight = 13252.527| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.34 r_work: 0.2983 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 13433 Z= 0.309 Angle : 0.751 9.490 18212 Z= 0.379 Chirality : 0.051 0.159 2156 Planarity : 0.007 0.069 2301 Dihedral : 9.010 89.812 1921 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 6.33 % Allowed : 18.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.20), residues: 1684 helix: 1.51 (0.17), residues: 833 sheet: 0.06 (0.30), residues: 282 loop : 0.26 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 201 HIS 0.008 0.002 HIS C 265 PHE 0.025 0.003 PHE C 619 TYR 0.017 0.003 TYR D 205 ARG 0.006 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.06496 ( 771) hydrogen bonds : angle 5.08728 ( 2229) covalent geometry : bond 0.00757 (13433) covalent geometry : angle 0.75125 (18212) *********************** 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 259 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 166 time to evaluate : 1.509 Fit side-chains REVERT: A 236 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.7008 (pp20) REVERT: A 299 GLN cc_start: 0.7903 (mm-40) cc_final: 0.6941 (tm-30) REVERT: B 75 GLN cc_start: 0.7331 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: B 263 LYS cc_start: 0.8213 (mttm) cc_final: 0.7807 (mtmt) REVERT: B 369 GLU cc_start: 0.5982 (OUTLIER) cc_final: 0.4943 (tt0) REVERT: B 387 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6258 (tmm) REVERT: C 98 ARG cc_start: 0.7723 (mmt-90) cc_final: 0.7415 (mmt90) REVERT: C 118 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7263 (mm-30) REVERT: C 170 ARG cc_start: 0.6742 (tpm170) cc_final: 0.6080 (mtt90) REVERT: C 208 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7036 (tmm160) REVERT: C 312 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7373 (ttp80) REVERT: C 320 ARG cc_start: 0.7943 (ttm170) cc_final: 0.7677 (tpp80) REVERT: C 361 ASP cc_start: 0.7590 (t0) cc_final: 0.7224 (t0) REVERT: C 420 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6597 (mm-40) REVERT: C 527 ARG cc_start: 0.8487 (mtp180) cc_final: 0.7683 (mtt90) REVERT: C 557 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8230 (mtp) REVERT: C 574 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7911 (ttp-110) REVERT: D 216 LYS cc_start: 0.8552 (mtpp) cc_final: 0.7889 (mtmm) REVERT: D 314 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7204 (ttm110) REVERT: D 420 GLN cc_start: 0.7467 (tt0) cc_final: 0.7105 (tm-30) outliers start: 93 outliers final: 40 residues processed: 232 average time/residue: 1.4923 time to fit residues: 374.8580 Evaluate side-chains 213 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 163 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 86 LEU Chi-restraints excluded: chain A residue 102 SER 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 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 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 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 312 ARG 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 118 optimal weight: 0.0010 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 151 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 D 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.130293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.107109 restraints weight = 13044.113| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.35 r_work: 0.3068 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13433 Z= 0.109 Angle : 0.513 6.112 18212 Z= 0.265 Chirality : 0.040 0.148 2156 Planarity : 0.005 0.070 2301 Dihedral : 7.281 87.128 1884 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 4.29 % Allowed : 20.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.20), residues: 1684 helix: 2.18 (0.18), residues: 833 sheet: 0.27 (0.31), residues: 267 loop : 0.30 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 148 HIS 0.003 0.001 HIS A 120 PHE 0.015 0.001 PHE B 136 TYR 0.011 0.001 TYR D 205 ARG 0.004 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 771) hydrogen bonds : angle 4.52959 ( 2229) covalent geometry : bond 0.00228 (13433) covalent geometry : angle 0.51261 (18212) *********************** 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 243 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 2.255 Fit side-chains REVERT: A 236 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.6996 (pp20) REVERT: A 299 GLN cc_start: 0.7846 (mm-40) cc_final: 0.6875 (tm-30) REVERT: A 369 GLU cc_start: 0.7010 (mp0) cc_final: 0.6192 (pm20) REVERT: B 13 SER cc_start: 0.8309 (t) cc_final: 0.8103 (p) REVERT: B 75 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.6865 (tt0) REVERT: B 263 LYS cc_start: 0.8142 (mttm) cc_final: 0.7781 (mtmt) REVERT: B 369 GLU cc_start: 0.5805 (OUTLIER) cc_final: 0.4904 (tt0) REVERT: B 387 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6197 (tmm) REVERT: C 98 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7358 (mmt90) REVERT: C 118 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7025 (mt-10) REVERT: C 170 ARG cc_start: 0.6544 (tpm170) cc_final: 0.5932 (mtt90) REVERT: C 208 ARG cc_start: 0.8048 (ttt180) cc_final: 0.6926 (tmm160) REVERT: C 213 LEU cc_start: 0.8130 (mp) cc_final: 0.7785 (mt) REVERT: C 311 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8000 (mp) REVERT: C 312 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7378 (ttp80) REVERT: C 314 ARG cc_start: 0.7926 (tpt170) cc_final: 0.6833 (ttt180) REVERT: C 320 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7655 (tpp80) REVERT: C 420 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.6656 (mm-40) REVERT: C 527 ARG cc_start: 0.8375 (mtp180) cc_final: 0.7555 (mtt90) REVERT: C 535 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7833 (mmp) REVERT: C 557 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8072 (mtp) REVERT: C 574 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7864 (ttm170) REVERT: D 119 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7563 (p) REVERT: D 149 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7870 (mt-10) REVERT: D 157 ASP cc_start: 0.8093 (m-30) cc_final: 0.7845 (m-30) REVERT: D 216 LYS cc_start: 0.8420 (mtpp) cc_final: 0.7766 (mtmm) REVERT: D 314 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7203 (ttp-170) REVERT: D 420 GLN cc_start: 0.7416 (tt0) cc_final: 0.7082 (tm-30) REVERT: D 511 ARG cc_start: 0.6917 (mmm160) cc_final: 0.6685 (mtp85) REVERT: D 543 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7987 (mp0) outliers start: 63 outliers final: 31 residues processed: 221 average time/residue: 1.8396 time to fit residues: 439.1107 Evaluate side-chains 213 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 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 115 VAL Chi-restraints excluded: chain B residue 246 THR 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 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 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 311 LEU 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 C residue 574 ARG 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 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 146 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 115 optimal weight: 0.0980 chunk 137 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 A 380 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.104083 restraints weight = 12993.602| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.35 r_work: 0.3027 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13433 Z= 0.187 Angle : 0.601 8.413 18212 Z= 0.306 Chirality : 0.044 0.211 2156 Planarity : 0.005 0.065 2301 Dihedral : 7.132 88.281 1874 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.17 % Allowed : 20.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.20), residues: 1684 helix: 2.07 (0.17), residues: 833 sheet: 0.17 (0.31), residues: 267 loop : 0.26 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 201 HIS 0.005 0.001 HIS D 265 PHE 0.021 0.002 PHE C 619 TYR 0.018 0.002 TYR D 205 ARG 0.004 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 771) hydrogen bonds : angle 4.66309 ( 2229) covalent geometry : bond 0.00448 (13433) covalent geometry : angle 0.60147 (18212) *********************** 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 252 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 176 time to evaluate : 1.369 Fit side-chains REVERT: A 141 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8689 (mttt) REVERT: A 236 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8125 (pp20) REVERT: A 299 GLN cc_start: 0.7865 (mm-40) cc_final: 0.6881 (tm-30) REVERT: B 5 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.6934 (tpp) REVERT: B 13 SER cc_start: 0.8418 (t) cc_final: 0.8184 (p) REVERT: B 35 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7452 (ttm-80) REVERT: B 263 LYS cc_start: 0.8156 (mttm) cc_final: 0.7791 (mtmt) REVERT: B 369 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.4949 (tt0) REVERT: B 387 MET cc_start: 0.6658 (OUTLIER) cc_final: 0.6054 (tmm) REVERT: C 98 ARG cc_start: 0.7666 (mmt-90) cc_final: 0.7354 (mmt90) REVERT: C 118 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: C 170 ARG cc_start: 0.6671 (tpm170) cc_final: 0.6072 (mtt90) REVERT: C 208 ARG cc_start: 0.8072 (ttt180) cc_final: 0.6953 (tmm160) REVERT: C 312 ARG cc_start: 0.8082 (ttp-170) cc_final: 0.7386 (ttp80) REVERT: C 320 ARG cc_start: 0.7901 (ttm170) cc_final: 0.7648 (tpp80) REVERT: C 393 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7126 (ptm160) REVERT: C 420 GLN cc_start: 0.7392 (OUTLIER) cc_final: 0.6640 (mm-40) REVERT: C 527 ARG cc_start: 0.8403 (mtp180) cc_final: 0.7584 (mtt90) REVERT: C 557 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8178 (mtp) REVERT: D 216 LYS cc_start: 0.8508 (mtpp) cc_final: 0.7847 (mtmm) REVERT: D 314 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7140 (ttm110) REVERT: D 420 GLN cc_start: 0.7426 (tt0) cc_final: 0.7092 (tm-30) REVERT: D 511 ARG cc_start: 0.6923 (mmm160) cc_final: 0.6699 (mtp85) REVERT: D 543 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7103 (mm-30) outliers start: 76 outliers final: 43 residues processed: 224 average time/residue: 1.5391 time to fit residues: 370.7360 Evaluate side-chains 227 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 172 time to evaluate : 1.517 ------------------------------------------------------------------------------- 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 236 GLU 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 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 115 VAL 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 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 393 ARG 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 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 389 SER 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 92 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 77 optimal weight: 8.9990 chunk 38 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 75 GLN D 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.127567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.104070 restraints weight = 13237.600| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.36 r_work: 0.3035 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13433 Z= 0.115 Angle : 0.512 7.131 18212 Z= 0.264 Chirality : 0.040 0.146 2156 Planarity : 0.005 0.068 2301 Dihedral : 6.766 86.902 1870 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 4.35 % Allowed : 20.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.20), residues: 1684 helix: 2.32 (0.18), residues: 839 sheet: 0.19 (0.31), residues: 267 loop : 0.33 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 201 HIS 0.003 0.001 HIS A 120 PHE 0.015 0.002 PHE B 136 TYR 0.014 0.002 TYR D 205 ARG 0.002 0.000 ARG C 546 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 771) hydrogen bonds : angle 4.42442 ( 2229) covalent geometry : bond 0.00259 (13433) covalent geometry : angle 0.51243 (18212) *********************** 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 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 1.663 Fit side-chains REVERT: A 75 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: A 141 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8670 (mttt) REVERT: A 299 GLN cc_start: 0.7887 (mm-40) cc_final: 0.6937 (tm-30) REVERT: B 13 SER cc_start: 0.8339 (t) cc_final: 0.8131 (p) REVERT: B 102 SER cc_start: 0.8905 (OUTLIER) cc_final: 0.8560 (m) REVERT: B 170 HIS cc_start: 0.8952 (m90) cc_final: 0.8746 (m-70) REVERT: B 263 LYS cc_start: 0.8136 (mttm) cc_final: 0.7794 (mtmt) REVERT: B 369 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.4613 (mp0) REVERT: B 387 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6099 (tmm) REVERT: C 98 ARG cc_start: 0.7689 (mmt-90) cc_final: 0.7374 (mmt90) REVERT: C 118 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7158 (mt-10) REVERT: C 119 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7782 (m) REVERT: C 170 ARG cc_start: 0.6686 (OUTLIER) cc_final: 0.6095 (mtt90) REVERT: C 208 ARG cc_start: 0.8016 (ttt180) cc_final: 0.6923 (tmm160) REVERT: C 213 LEU cc_start: 0.8111 (mp) cc_final: 0.7752 (mt) REVERT: C 311 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7989 (mp) REVERT: C 312 ARG cc_start: 0.8019 (ttp-170) cc_final: 0.7328 (ttp80) REVERT: C 320 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7667 (tpp80) REVERT: C 420 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.6716 (mm-40) REVERT: C 527 ARG cc_start: 0.8398 (mtp180) cc_final: 0.7612 (mtt90) REVERT: C 557 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.8015 (mmm) REVERT: D 119 SER cc_start: 0.8034 (OUTLIER) cc_final: 0.7585 (p) REVERT: D 149 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 188 ARG cc_start: 0.8223 (mtm110) cc_final: 0.8013 (mtm-85) REVERT: D 216 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7802 (mtmm) REVERT: D 314 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7168 (ttm110) REVERT: D 420 GLN cc_start: 0.7429 (tt0) cc_final: 0.7191 (tm-30) REVERT: D 511 ARG cc_start: 0.6930 (mmm160) cc_final: 0.6711 (mtp85) REVERT: D 543 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8022 (mp0) outliers start: 64 outliers final: 34 residues processed: 219 average time/residue: 1.9866 time to fit residues: 471.0621 Evaluate side-chains 221 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 173 time to evaluate : 2.766 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain A residue 376 THR 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 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 119 SER 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 225 VAL Chi-restraints excluded: chain C residue 231 GLN Chi-restraints excluded: chain C residue 258 GLU 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 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 226 ASP 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 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 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 103 optimal weight: 0.7980 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 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 = 0.3319 r_free = 0.3319 target = 0.124278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.100663 restraints weight = 13383.588| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.34 r_work: 0.2981 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13433 Z= 0.203 Angle : 0.616 7.715 18212 Z= 0.313 Chirality : 0.045 0.155 2156 Planarity : 0.005 0.065 2301 Dihedral : 6.827 88.350 1865 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 5.58 % Allowed : 19.39 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1684 helix: 2.05 (0.17), residues: 840 sheet: 0.12 (0.31), residues: 267 loop : 0.27 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 201 HIS 0.005 0.001 HIS D 265 PHE 0.022 0.002 PHE C 619 TYR 0.021 0.002 TYR D 205 ARG 0.003 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.05110 ( 771) hydrogen bonds : angle 4.64394 ( 2229) covalent geometry : bond 0.00492 (13433) covalent geometry : angle 0.61605 (18212) *********************** 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 256 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 174 time to evaluate : 1.427 Fit side-chains REVERT: A 75 GLN cc_start: 0.6752 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: A 141 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8720 (mttt) REVERT: A 299 GLN cc_start: 0.7845 (mm-40) cc_final: 0.6912 (tm-30) REVERT: B 5 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.6930 (tpp) REVERT: B 13 SER cc_start: 0.8447 (t) cc_final: 0.8212 (p) REVERT: B 35 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7368 (ttm-80) REVERT: B 57 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8372 (tt) REVERT: B 263 LYS cc_start: 0.8165 (mttm) cc_final: 0.7807 (mtmt) REVERT: B 369 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.4957 (tt0) REVERT: B 387 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6118 (tmm) REVERT: C 98 ARG cc_start: 0.7699 (mmt-90) cc_final: 0.7387 (mmt90) REVERT: C 118 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: C 170 ARG cc_start: 0.6804 (tpm170) cc_final: 0.6209 (mtt90) REVERT: C 208 ARG cc_start: 0.8094 (ttt180) cc_final: 0.6997 (tmm160) REVERT: C 312 ARG cc_start: 0.8114 (ttp-170) cc_final: 0.7445 (ttp80) REVERT: C 320 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7669 (tpp80) REVERT: C 420 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.6649 (mm-40) REVERT: C 527 ARG cc_start: 0.8440 (mtp180) cc_final: 0.7684 (mtt90) REVERT: C 557 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8177 (mtp) REVERT: D 216 LYS cc_start: 0.8550 (mtpp) cc_final: 0.7911 (mtmm) REVERT: D 314 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7208 (ttm110) REVERT: D 420 GLN cc_start: 0.7489 (tt0) cc_final: 0.7178 (tm-30) outliers start: 82 outliers final: 50 residues processed: 226 average time/residue: 1.5149 time to fit residues: 368.7541 Evaluate side-chains 233 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 1.588 ------------------------------------------------------------------------------- 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 86 LEU 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 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 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 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 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 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 226 ASP 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 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 86 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 46 optimal weight: 0.0770 chunk 9 optimal weight: 3.9990 chunk 157 optimal weight: 0.5980 chunk 166 optimal weight: 0.7980 chunk 129 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.130886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107772 restraints weight = 13026.370| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.33 r_work: 0.3066 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13433 Z= 0.099 Angle : 0.485 6.584 18212 Z= 0.252 Chirality : 0.039 0.141 2156 Planarity : 0.005 0.069 2301 Dihedral : 6.274 86.159 1865 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.01 % Allowed : 21.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.20), residues: 1684 helix: 2.50 (0.17), residues: 837 sheet: 0.23 (0.31), residues: 267 loop : 0.39 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 148 HIS 0.004 0.000 HIS A 120 PHE 0.014 0.001 PHE B 136 TYR 0.013 0.001 TYR D 205 ARG 0.003 0.000 ARG D 188 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 771) hydrogen bonds : angle 4.28507 ( 2229) covalent geometry : bond 0.00209 (13433) covalent geometry : angle 0.48534 (18212) *********************** 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 242 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 183 time to evaluate : 1.520 Fit side-chains REVERT: A 102 SER cc_start: 0.8883 (OUTLIER) cc_final: 0.8648 (m) REVERT: A 141 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8654 (mttt) REVERT: A 299 GLN cc_start: 0.7844 (mm-40) cc_final: 0.6896 (tm-30) REVERT: A 369 GLU cc_start: 0.6932 (mp0) cc_final: 0.6091 (pm20) REVERT: B 13 SER cc_start: 0.8283 (t) cc_final: 0.8032 (p) REVERT: B 170 HIS cc_start: 0.8947 (m90) cc_final: 0.8736 (m-70) REVERT: B 263 LYS cc_start: 0.8124 (mttm) cc_final: 0.7736 (mtmt) REVERT: B 369 GLU cc_start: 0.5740 (OUTLIER) cc_final: 0.4651 (mp0) REVERT: B 387 MET cc_start: 0.6634 (OUTLIER) cc_final: 0.6070 (tmm) REVERT: C 98 ARG cc_start: 0.7690 (mmt-90) cc_final: 0.7371 (mmt90) REVERT: C 118 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7027 (mt-10) REVERT: C 170 ARG cc_start: 0.6674 (OUTLIER) cc_final: 0.6141 (mtt90) REVERT: C 208 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7101 (ttp-110) REVERT: C 213 LEU cc_start: 0.8086 (mp) cc_final: 0.7725 (mt) REVERT: C 311 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 312 ARG cc_start: 0.8043 (ttp-170) cc_final: 0.7322 (ttp80) REVERT: C 314 ARG cc_start: 0.7922 (tpt170) cc_final: 0.6874 (ttt180) REVERT: C 320 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7673 (tpp80) REVERT: C 420 GLN cc_start: 0.7434 (OUTLIER) cc_final: 0.6721 (mm-40) REVERT: C 527 ARG cc_start: 0.8386 (mtp180) cc_final: 0.7604 (mtt90) REVERT: C 557 MET cc_start: 0.8257 (mtt) cc_final: 0.8055 (mmm) REVERT: D 119 SER cc_start: 0.8000 (OUTLIER) cc_final: 0.7604 (p) REVERT: D 130 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8067 (m) REVERT: D 216 LYS cc_start: 0.8442 (mtpp) cc_final: 0.8218 (mttp) REVERT: D 314 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7274 (ttp-170) REVERT: D 420 GLN cc_start: 0.7463 (tt0) cc_final: 0.7228 (tm-30) REVERT: D 543 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8003 (mp0) outliers start: 59 outliers final: 34 residues processed: 222 average time/residue: 1.5144 time to fit residues: 361.7215 Evaluate side-chains 216 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 324 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain B residue 24 GLU 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 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 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 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 226 ASP Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 335 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 75 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 126 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 D 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.126717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.103313 restraints weight = 13185.203| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.36 r_work: 0.3017 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13433 Z= 0.217 Angle : 0.633 7.710 18212 Z= 0.321 Chirality : 0.046 0.155 2156 Planarity : 0.006 0.063 2301 Dihedral : 6.801 88.522 1865 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.63 % Allowed : 20.27 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1684 helix: 2.12 (0.17), residues: 834 sheet: 0.11 (0.31), residues: 267 loop : 0.29 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 201 HIS 0.005 0.001 HIS D 265 PHE 0.023 0.003 PHE D 619 TYR 0.021 0.002 TYR D 205 ARG 0.005 0.000 ARG C 546 Details of bonding type rmsd hydrogen bonds : bond 0.05247 ( 771) hydrogen bonds : angle 4.64619 ( 2229) covalent geometry : bond 0.00526 (13433) covalent geometry : angle 0.63320 (18212) *********************** 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 239 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 1.481 Fit side-chains REVERT: A 141 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8696 (mttt) REVERT: A 299 GLN cc_start: 0.7843 (mm-40) cc_final: 0.6880 (tm-30) REVERT: B 57 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8348 (tt) REVERT: B 263 LYS cc_start: 0.8188 (mttm) cc_final: 0.7826 (mtmt) REVERT: B 369 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.4940 (tt0) REVERT: B 387 MET cc_start: 0.6660 (OUTLIER) cc_final: 0.6053 (tmm) REVERT: C 98 ARG cc_start: 0.7704 (mmt-90) cc_final: 0.7392 (mmt90) REVERT: C 118 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: C 170 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6139 (mtt90) REVERT: C 208 ARG cc_start: 0.8118 (ttt180) cc_final: 0.7175 (ttp-110) REVERT: C 312 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7411 (ttp80) REVERT: C 320 ARG cc_start: 0.7926 (ttm170) cc_final: 0.7672 (tpp80) REVERT: C 420 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.6657 (mm-40) REVERT: C 527 ARG cc_start: 0.8433 (mtp180) cc_final: 0.7640 (mtt90) REVERT: C 557 MET cc_start: 0.8420 (mtt) cc_final: 0.8140 (mtp) REVERT: C 574 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7909 (ttp-110) REVERT: D 216 LYS cc_start: 0.8523 (mtpp) cc_final: 0.8294 (mttp) REVERT: D 314 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7154 (ttm110) REVERT: D 420 GLN cc_start: 0.7445 (tt0) cc_final: 0.7114 (tm-30) outliers start: 68 outliers final: 45 residues processed: 213 average time/residue: 1.5226 time to fit residues: 349.2777 Evaluate side-chains 224 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 170 time to evaluate : 1.425 ------------------------------------------------------------------------------- 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 293 VAL Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR 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 289 HIS 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 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 574 ARG 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 226 ASP 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 425 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 5 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 163 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN B 72 GLN B 75 GLN C 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.129335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.105738 restraints weight = 12891.591| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 1.39 r_work: 0.3040 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13433 Z= 0.117 Angle : 0.518 6.887 18212 Z= 0.267 Chirality : 0.040 0.143 2156 Planarity : 0.005 0.069 2301 Dihedral : 6.399 86.985 1865 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.88 % Allowed : 21.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.20), residues: 1684 helix: 2.34 (0.17), residues: 841 sheet: 0.19 (0.31), residues: 267 loop : 0.35 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 201 HIS 0.004 0.001 HIS A 120 PHE 0.016 0.002 PHE B 136 TYR 0.016 0.002 TYR D 205 ARG 0.006 0.000 ARG C 546 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 771) hydrogen bonds : angle 4.38342 ( 2229) covalent geometry : bond 0.00264 (13433) covalent geometry : angle 0.51810 (18212) *********************** 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 237 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 180 time to evaluate : 1.566 Fit side-chains REVERT: A 141 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8663 (mttt) REVERT: A 299 GLN cc_start: 0.7820 (mm-40) cc_final: 0.6880 (tm-30) REVERT: A 369 GLU cc_start: 0.6933 (mp0) cc_final: 0.6146 (pm20) REVERT: B 13 SER cc_start: 0.8286 (t) cc_final: 0.8047 (p) REVERT: B 57 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8309 (tt) REVERT: B 102 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8531 (m) REVERT: B 263 LYS cc_start: 0.8116 (mttm) cc_final: 0.7721 (mtmt) REVERT: B 369 GLU cc_start: 0.5752 (OUTLIER) cc_final: 0.4629 (mp0) REVERT: B 387 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.5995 (tmm) REVERT: C 98 ARG cc_start: 0.7656 (mmt-90) cc_final: 0.7340 (mmt90) REVERT: C 118 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7124 (mt-10) REVERT: C 170 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6129 (mtt90) REVERT: C 208 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7076 (ttp-110) REVERT: C 213 LEU cc_start: 0.8043 (mp) cc_final: 0.7702 (mt) REVERT: C 312 ARG cc_start: 0.8038 (ttp-170) cc_final: 0.7280 (ttp80) REVERT: C 320 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7669 (tpp80) REVERT: C 420 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.6689 (mm-40) REVERT: C 527 ARG cc_start: 0.8384 (mtp180) cc_final: 0.7570 (mtt90) REVERT: C 557 MET cc_start: 0.8294 (mtt) cc_final: 0.8071 (mmm) REVERT: C 574 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7700 (ttp-110) REVERT: D 119 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7578 (p) REVERT: D 130 SER cc_start: 0.8315 (OUTLIER) cc_final: 0.8064 (m) REVERT: D 216 LYS cc_start: 0.8440 (mtpp) cc_final: 0.8216 (mttp) REVERT: D 314 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7184 (ttp-170) REVERT: D 420 GLN cc_start: 0.7405 (tt0) cc_final: 0.7154 (tm-30) REVERT: D 543 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7016 (mm-30) outliers start: 57 outliers final: 39 residues processed: 216 average time/residue: 1.5246 time to fit residues: 354.4219 Evaluate side-chains 228 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 1.406 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain A residue 376 THR 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 289 HIS 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 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 574 ARG 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 226 ASP 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 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 170 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 76 optimal weight: 0.0030 chunk 166 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.0020 chunk 125 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.130409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106871 restraints weight = 12873.635| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.39 r_work: 0.3019 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1031 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= 0.105 Angle : 0.502 6.566 18212 Z= 0.259 Chirality : 0.040 0.142 2156 Planarity : 0.005 0.064 2301 Dihedral : 6.201 85.919 1865 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.54 % Allowed : 21.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.20), residues: 1684 helix: 2.50 (0.17), residues: 840 sheet: 0.21 (0.31), residues: 267 loop : 0.41 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 148 HIS 0.004 0.001 HIS A 120 PHE 0.014 0.001 PHE B 136 TYR 0.018 0.001 TYR D 205 ARG 0.007 0.000 ARG C 546 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 771) hydrogen bonds : angle 4.28456 ( 2229) covalent geometry : bond 0.00232 (13433) covalent geometry : angle 0.50168 (18212) ********************** 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 235 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 183 time to evaluate : 1.507 Fit side-chains REVERT: A 33 THR cc_start: 0.8255 (t) cc_final: 0.8010 (p) REVERT: A 141 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8634 (mttt) REVERT: A 299 GLN cc_start: 0.7856 (mm-40) cc_final: 0.6840 (tm-30) REVERT: A 369 GLU cc_start: 0.6894 (mp0) cc_final: 0.6087 (pm20) REVERT: B 13 SER cc_start: 0.8247 (t) cc_final: 0.8010 (p) REVERT: B 57 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8307 (tt) REVERT: B 170 HIS cc_start: 0.8918 (m90) cc_final: 0.8709 (m-70) REVERT: B 263 LYS cc_start: 0.8157 (mttm) cc_final: 0.7756 (mtmt) REVERT: B 369 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.4643 (mp0) REVERT: B 387 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.5989 (tmm) REVERT: C 98 ARG cc_start: 0.7650 (mmt-90) cc_final: 0.7334 (mmt90) REVERT: C 118 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: C 170 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6112 (mtt90) REVERT: C 208 ARG cc_start: 0.8016 (ttt180) cc_final: 0.7066 (ttp-110) REVERT: C 213 LEU cc_start: 0.8028 (mp) cc_final: 0.7685 (mt) REVERT: C 312 ARG cc_start: 0.8018 (ttp-170) cc_final: 0.7241 (ttp80) REVERT: C 314 ARG cc_start: 0.7905 (tpt170) cc_final: 0.6816 (ttt180) REVERT: C 320 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7667 (tpp80) REVERT: C 420 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.6706 (mm-40) REVERT: C 527 ARG cc_start: 0.8399 (mtp180) cc_final: 0.7580 (mtt90) REVERT: C 574 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7660 (ttp-110) REVERT: D 119 SER cc_start: 0.7991 (OUTLIER) cc_final: 0.7592 (p) REVERT: D 130 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.8030 (m) REVERT: D 216 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8208 (mttp) REVERT: D 314 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7229 (ttp-170) REVERT: D 420 GLN cc_start: 0.7446 (tt0) cc_final: 0.7198 (tm-30) REVERT: D 543 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7993 (mp0) outliers start: 52 outliers final: 35 residues processed: 218 average time/residue: 1.5487 time to fit residues: 364.4729 Evaluate side-chains 225 residues out of total 1470 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 324 SER Chi-restraints excluded: chain A residue 376 THR 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 289 HIS 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 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 574 ARG 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 133 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 158 optimal weight: 2.9990 chunk 34 optimal weight: 0.0670 chunk 119 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 67 optimal weight: 0.0020 chunk 110 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.4526 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN B 75 GLN C 126 GLN C 262 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.132046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108605 restraints weight = 12964.865| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.40 r_work: 0.3079 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1142 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= 0.098 Angle : 0.485 6.296 18212 Z= 0.250 Chirality : 0.039 0.141 2156 Planarity : 0.005 0.065 2301 Dihedral : 5.934 83.929 1864 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.20 % Allowed : 22.31 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.20), residues: 1684 helix: 2.67 (0.17), residues: 834 sheet: 0.23 (0.32), residues: 269 loop : 0.47 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 148 HIS 0.004 0.001 HIS A 120 PHE 0.014 0.001 PHE B 136 TYR 0.019 0.001 TYR D 205 ARG 0.007 0.000 ARG C 546 Details of bonding type rmsd hydrogen bonds : bond 0.03568 ( 771) hydrogen bonds : angle 4.16363 ( 2229) covalent geometry : bond 0.00216 (13433) covalent geometry : angle 0.48539 (18212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10650.74 seconds wall clock time: 185 minutes 16.38 seconds (11116.38 seconds total)