Starting phenix.real_space_refine on Thu Aug 6 05:37:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9w_45374/08_2026/9c9w_45374_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9w_45374/08_2026/9c9w_45374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9w_45374/08_2026/9c9w_45374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9w_45374/08_2026/9c9w_45374.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9w_45374/08_2026/9c9w_45374_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9w_45374/08_2026/9c9w_45374_neut.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 80 5.49 5 S 78 5.16 5 C 8443 2.51 5 N 2385 2.21 5 O 2774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13761 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4841 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 475 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.78, per 1000 atoms: 0.20 Number of scatterers: 13761 At special positions: 0 Unit cell: (92.96, 140.27, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 78 16.00 P 80 15.00 O 2774 8.00 N 2385 7.00 C 8443 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 386.6 milliseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 42.4% alpha, 15.7% beta 25 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 10 through 23 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.683A pdb=" N PHE A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 119 through 134 removed outlier: 3.638A pdb=" N ALA A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 156 through 166 removed outlier: 3.962A pdb=" N ALA A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 200 Processing helix chain 'A' and resid 217 through 235 removed outlier: 5.067A pdb=" N ARG A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N HIS A 229 " --> pdb=" O CYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 364 through 372 Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 450 through 455 Processing helix chain 'A' and resid 495 through 507 Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 538 through 552 removed outlier: 3.775A pdb=" N ILE A 551 " --> pdb=" O GLY A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 568 Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.597A pdb=" N VAL A 581 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 585 " --> pdb=" O VAL A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 611 Processing helix chain 'B' and resid 2 through 13 removed outlier: 3.950A pdb=" N ALA B 12 " --> pdb=" O ALA B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 24 Processing helix chain 'B' and resid 33 through 41 removed outlier: 4.190A pdb=" N ILE B 37 " --> pdb=" O VAL B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 49 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 68 through 73 removed outlier: 3.879A pdb=" N TRP C 73 " --> pdb=" O TYR C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 93 through 96 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 122 through 134 Processing helix chain 'C' and resid 156 through 166 Processing helix chain 'C' and resid 171 through 204 removed outlier: 3.908A pdb=" N SER C 177 " --> pdb=" O ASN C 173 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 178 " --> pdb=" O GLU C 174 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALA C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ARG C 194 " --> pdb=" O CYS C 190 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYS C 203 " --> pdb=" O TYR C 199 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 204 " --> pdb=" O PHE C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 208 Processing helix chain 'C' and resid 217 through 234 removed outlier: 4.195A pdb=" N CYS C 225 " --> pdb=" O THR C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.475A pdb=" N LEU C 279 " --> pdb=" O ASN C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 315 Processing helix chain 'C' and resid 317 through 332 Processing helix chain 'C' and resid 349 through 357 removed outlier: 3.533A pdb=" N SER C 353 " --> pdb=" O ASP C 349 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 374 removed outlier: 3.664A pdb=" N ALA C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU C 373 " --> pdb=" O ARG C 369 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY C 374 " --> pdb=" O LEU C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.526A pdb=" N GLU C 400 " --> pdb=" O THR C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 removed outlier: 3.760A pdb=" N GLU C 410 " --> pdb=" O TRP C 406 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 Processing helix chain 'C' and resid 456 through 460 Processing helix chain 'C' and resid 495 through 505 Processing helix chain 'C' and resid 512 through 524 removed outlier: 4.053A pdb=" N VAL C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 552 removed outlier: 3.747A pdb=" N GLY C 547 " --> pdb=" O VAL C 543 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 556 Processing helix chain 'C' and resid 559 through 573 removed outlier: 4.276A pdb=" N LEU C 570 " --> pdb=" O LYS C 566 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE C 571 " --> pdb=" O GLN C 567 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 599 Processing helix chain 'C' and resid 600 through 611 removed outlier: 3.833A pdb=" N VAL C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N SER C 610 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C 611 " --> pdb=" O MET C 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 17 through 25 Processing helix chain 'D' and resid 32 through 43 Processing helix chain 'D' and resid 44 through 49 removed outlier: 3.964A pdb=" N ILE D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 7.297A pdb=" N LYS A 2 " --> pdb=" O ARG A 51 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS A 53 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N VAL A 4 " --> pdb=" O LYS A 53 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N THR A 55 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N MET A 6 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR A 111 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 242 through 247 removed outlier: 3.907A pdb=" N GLU A 480 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 284 through 295 removed outlier: 5.649A pdb=" N VAL A 285 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG A 434 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 287 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS A 293 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 426 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS A 424 " --> pdb=" O LYS A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 64 through 65 Processing sheet with id=AA5, first strand: chain 'B' and resid 140 through 142 removed outlier: 6.687A pdb=" N THR B 107 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N LEU B 142 " --> pdb=" O THR B 107 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 109 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU B 95 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 75 " --> pdb=" O GLN B 98 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR B 100 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N ILE B 73 " --> pdb=" O THR B 100 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.111A pdb=" N SER C 37 " --> pdb=" O SER C 56 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N SER C 56 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL C 4 " --> pdb=" O LYS C 53 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR C 55 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N MET C 6 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL C 7 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE C 112 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 63 through 66 Processing sheet with id=AA8, first strand: chain 'C' and resid 255 through 256 removed outlier: 3.666A pdb=" N LYS C 486 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 480 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 283 " --> pdb=" O PHE C 476 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 284 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER C 432 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C 288 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 430 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LYS C 425 " --> pdb=" O LEU C 448 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 255 through 256 removed outlier: 3.666A pdb=" N LYS C 486 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 480 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA C 283 " --> pdb=" O PHE C 476 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN C 284 " --> pdb=" O ARG C 434 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER C 432 " --> pdb=" O GLU C 286 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C 288 " --> pdb=" O THR C 430 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 430 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS C 291 " --> pdb=" O GLN C 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 527 through 529 Processing sheet with id=AB2, first strand: chain 'D' and resid 64 through 65 removed outlier: 4.401A pdb=" N ASP D 134 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG D 96 " --> pdb=" O ILE D 76 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ILE D 76 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN D 98 " --> pdb=" O GLN D 74 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR D 125 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS D 126 " --> pdb=" O LEU D 150 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 60 hydrogen bonds 120 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 51 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3834 1.33 - 1.45: 2725 1.45 - 1.57: 7367 1.57 - 1.69: 155 1.69 - 1.81: 123 Bond restraints: 14204 Sorted by residual: bond pdb=" C SER C 335 " pdb=" N PTR C 336 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.21e+01 bond pdb=" C1' DC L 31 " pdb=" N1 DC L 31 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.61e+01 bond pdb=" C3' DT E 6 " pdb=" C2' DT E 6 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" N GLN A 331 " pdb=" CA GLN A 331 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.35e-02 5.49e+03 1.18e+01 bond pdb=" C3' DA E 19 " pdb=" C2' DA E 19 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 14199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 19536 5.75 - 11.51: 21 11.51 - 17.26: 3 17.26 - 23.01: 1 23.01 - 28.76: 1 Bond angle restraints: 19562 Sorted by residual: angle pdb=" O SER C 335 " pdb=" C SER C 335 " pdb=" N PTR C 336 " ideal model delta sigma weight residual 123.00 94.24 28.76 1.60e+00 3.91e-01 3.23e+02 angle pdb=" N GLN A 331 " pdb=" CA GLN A 331 " pdb=" C GLN A 331 " ideal model delta sigma weight residual 113.01 97.68 15.33 1.20e+00 6.94e-01 1.63e+02 angle pdb=" CA SER C 335 " pdb=" C SER C 335 " pdb=" N PTR C 336 " ideal model delta sigma weight residual 116.20 136.10 -19.90 2.00e+00 2.50e-01 9.90e+01 angle pdb=" C SER C 335 " pdb=" N PTR C 336 " pdb=" CA PTR C 336 " ideal model delta sigma weight residual 121.70 137.34 -15.64 1.80e+00 3.09e-01 7.55e+01 angle pdb=" O4' DA E 3 " pdb=" C4' DA E 3 " pdb=" C3' DA E 3 " ideal model delta sigma weight residual 106.00 102.47 3.53 6.00e-01 2.78e+00 3.45e+01 ... (remaining 19557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 7878 33.78 - 67.55: 503 67.55 - 101.33: 30 101.33 - 135.10: 0 135.10 - 168.88: 1 Dihedral angle restraints: 8412 sinusoidal: 3943 harmonic: 4469 Sorted by residual: dihedral pdb=" CA SER C 335 " pdb=" C SER C 335 " pdb=" N PTR C 336 " pdb=" CA PTR C 336 " ideal model delta harmonic sigma weight residual 180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA PRO A 491 " pdb=" C PRO A 491 " pdb=" N ASP A 492 " pdb=" CA ASP A 492 " ideal model delta harmonic sigma weight residual 180.00 148.58 31.42 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA ASN A 489 " pdb=" C ASN A 489 " pdb=" N PRO A 490 " pdb=" CA PRO A 490 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 8409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1620 0.045 - 0.091: 427 0.091 - 0.136: 131 0.136 - 0.182: 14 0.182 - 0.227: 3 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA GLN A 331 " pdb=" N GLN A 331 " pdb=" C GLN A 331 " pdb=" CB GLN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PHE A 195 " pdb=" N PHE A 195 " pdb=" C PHE A 195 " pdb=" CB PHE A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 25 " pdb=" CA THR B 25 " pdb=" OG1 THR B 25 " pdb=" CG2 THR B 25 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2192 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 335 " 0.066 2.00e-02 2.50e+03 1.04e-01 1.07e+02 pdb=" C SER C 335 " -0.179 2.00e-02 2.50e+03 pdb=" O SER C 335 " 0.053 2.00e-02 2.50e+03 pdb=" N PTR C 336 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 490 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO A 491 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG L 42 " -0.014 2.00e-02 2.50e+03 1.62e-02 7.92e+00 pdb=" N9 DG L 42 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG L 42 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG L 42 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG L 42 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG L 42 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG L 42 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG L 42 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG L 42 " 0.042 2.00e-02 2.50e+03 pdb=" N2 DG L 42 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DG L 42 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 42 " -0.001 2.00e-02 2.50e+03 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 266 2.64 - 3.20: 13015 3.20 - 3.77: 22012 3.77 - 4.33: 28704 4.33 - 4.90: 43519 Nonbonded interactions: 107516 Sorted by model distance: nonbonded pdb=" O PRO D 122 " pdb=" OG1 THR D 125 " model vdw 2.070 3.040 nonbonded pdb=" O3' DA E 24 " pdb="MN MN E 101 " model vdw 2.112 2.320 nonbonded pdb=" NH1 ARG C 149 " pdb=" O ALA C 150 " model vdw 2.143 3.120 nonbonded pdb=" O SER D 118 " pdb=" OG1 THR D 121 " model vdw 2.158 3.040 nonbonded pdb=" O VAL A 309 " pdb=" O SER A 312 " model vdw 2.164 3.040 ... (remaining 107511 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 0 through 335 or resid 337 through 611)) selection = (chain 'C' and (resid 0 through 335 or resid 337 through 611)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 3.050 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.950 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 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 : 0.006 0.476 14205 Z= 0.514 Angle : 0.841 28.764 19562 Z= 0.555 Chirality : 0.046 0.227 2195 Planarity : 0.005 0.104 2244 Dihedral : 19.220 168.878 5528 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.58 % Favored : 90.23 % Rotamer: Outliers : 0.15 % Allowed : 1.12 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1535 helix: -0.20 (0.21), residues: 581 sheet: -0.83 (0.35), residues: 224 loop : -1.75 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 308 TYR 0.026 0.002 TYR A 595 PHE 0.041 0.002 PHE A 589 TRP 0.023 0.002 TRP C 363 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.32 (14204) covalent geometry : angle 0.84108 / 0.56 (19562) hydrogen bonds : bond 0.16309 / 10.96 ( 580) hydrogen bonds : angle 6.96821 / 4.99 ( 1605) Misc. bond : bond 0.47641 / 25.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.8971 (mttt) cc_final: 0.8760 (mttp) REVERT: A 66 PHE cc_start: 0.7261 (m-80) cc_final: 0.7034 (m-80) REVERT: A 119 ASP cc_start: 0.8576 (p0) cc_final: 0.8287 (p0) REVERT: A 181 ARG cc_start: 0.8605 (ttt-90) cc_final: 0.8144 (ttp80) REVERT: A 222 LEU cc_start: 0.8734 (tp) cc_final: 0.8415 (tp) REVERT: A 226 VAL cc_start: 0.8755 (p) cc_final: 0.8498 (p) REVERT: A 231 LYS cc_start: 0.8839 (mptt) cc_final: 0.8547 (mptt) REVERT: A 260 ASP cc_start: 0.7533 (p0) cc_final: 0.7287 (p0) REVERT: A 272 MET cc_start: 0.7329 (mtt) cc_final: 0.6688 (mtt) REVERT: A 291 LYS cc_start: 0.8249 (mttt) cc_final: 0.8001 (mttt) REVERT: A 293 LYS cc_start: 0.7723 (pttm) cc_final: 0.6798 (pttm) REVERT: A 305 GLU cc_start: 0.8535 (tt0) cc_final: 0.7729 (tp30) REVERT: A 324 THR cc_start: 0.7850 (p) cc_final: 0.7620 (t) REVERT: A 326 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8145 (mt-10) REVERT: A 328 LEU cc_start: 0.7872 (mt) cc_final: 0.7638 (mt) REVERT: A 338 ARG cc_start: 0.8046 (tpp80) cc_final: 0.7779 (tpp80) REVERT: A 346 GLU cc_start: 0.7679 (mp0) cc_final: 0.7332 (mp0) REVERT: A 351 LYS cc_start: 0.8622 (tttp) cc_final: 0.8353 (tppt) REVERT: A 355 ARG cc_start: 0.8355 (tpm170) cc_final: 0.7792 (tpm170) REVERT: A 360 HIS cc_start: 0.8076 (t-90) cc_final: 0.7633 (t-90) REVERT: A 368 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8452 (mtpt) REVERT: A 379 ARG cc_start: 0.7474 (mtp85) cc_final: 0.7227 (mtp85) REVERT: A 380 LYS cc_start: 0.8209 (ttpt) cc_final: 0.7949 (ttmt) REVERT: A 408 LEU cc_start: 0.8681 (tp) cc_final: 0.8410 (tp) REVERT: A 409 TYR cc_start: 0.8443 (t80) cc_final: 0.8158 (t80) REVERT: A 414 ARG cc_start: 0.8766 (mtt-85) cc_final: 0.7608 (mtp180) REVERT: A 476 PHE cc_start: 0.7510 (m-80) cc_final: 0.7304 (m-80) REVERT: A 489 ASN cc_start: 0.6684 (p0) cc_final: 0.6261 (p0) REVERT: A 514 ILE cc_start: 0.9021 (mp) cc_final: 0.8809 (mp) REVERT: A 516 VAL cc_start: 0.8639 (m) cc_final: 0.8312 (p) REVERT: A 517 HIS cc_start: 0.8015 (m90) cc_final: 0.7667 (m90) REVERT: A 525 ASN cc_start: 0.6854 (m-40) cc_final: 0.6285 (m110) REVERT: A 526 TYR cc_start: 0.6707 (m-10) cc_final: 0.6139 (m-80) REVERT: B 71 LEU cc_start: 0.7729 (mt) cc_final: 0.6996 (mt) REVERT: B 96 ARG cc_start: 0.8335 (ttp-170) cc_final: 0.8134 (ttp-170) REVERT: C 4 VAL cc_start: 0.6556 (t) cc_final: 0.6316 (t) REVERT: C 13 LEU cc_start: 0.8959 (tp) cc_final: 0.8497 (tp) REVERT: C 32 LEU cc_start: 0.7790 (mt) cc_final: 0.7474 (mt) REVERT: C 53 LYS cc_start: 0.7873 (mppt) cc_final: 0.7106 (mppt) REVERT: C 71 ASN cc_start: 0.7545 (m110) cc_final: 0.7270 (m110) REVERT: C 95 LYS cc_start: 0.9031 (mppt) cc_final: 0.8494 (mppt) REVERT: C 139 LYS cc_start: 0.7201 (tmmt) cc_final: 0.6662 (tttm) REVERT: C 184 LEU cc_start: 0.8527 (tt) cc_final: 0.8258 (tp) REVERT: C 204 TYR cc_start: 0.7495 (m-80) cc_final: 0.7195 (m-10) REVERT: C 236 LYS cc_start: 0.8613 (mppt) cc_final: 0.8016 (mppt) REVERT: C 244 GLN cc_start: 0.5329 (tp-100) cc_final: 0.5059 (tp-100) REVERT: C 262 VAL cc_start: 0.8874 (m) cc_final: 0.8633 (p) REVERT: C 267 ARG cc_start: 0.7204 (tpm170) cc_final: 0.6927 (tpm170) REVERT: C 273 PHE cc_start: 0.7695 (m-10) cc_final: 0.7259 (m-10) REVERT: C 306 MET cc_start: 0.7864 (tmm) cc_final: 0.7436 (tmm) REVERT: C 307 LEU cc_start: 0.8759 (mt) cc_final: 0.8557 (mt) REVERT: C 314 LEU cc_start: 0.8196 (mp) cc_final: 0.7867 (mm) REVERT: C 326 GLU cc_start: 0.8425 (tp30) cc_final: 0.8223 (mm-30) REVERT: C 351 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8721 (ttpp) REVERT: C 357 GLN cc_start: 0.7689 (tt0) cc_final: 0.6910 (tt0) REVERT: C 368 LYS cc_start: 0.9121 (ttmm) cc_final: 0.8750 (mtpp) REVERT: C 410 GLU cc_start: 0.7949 (tt0) cc_final: 0.7586 (tt0) REVERT: C 415 HIS cc_start: 0.7988 (t-90) cc_final: 0.7592 (t-90) REVERT: C 419 THR cc_start: 0.8276 (m) cc_final: 0.8013 (m) REVERT: C 420 VAL cc_start: 0.8464 (m) cc_final: 0.8257 (t) REVERT: C 434 ARG cc_start: 0.6073 (mmm160) cc_final: 0.5184 (ttm-80) REVERT: C 438 GLU cc_start: 0.7881 (mm-30) cc_final: 0.6598 (tp30) REVERT: C 454 GLU cc_start: 0.7734 (pt0) cc_final: 0.7232 (pt0) REVERT: C 467 LEU cc_start: 0.8954 (mp) cc_final: 0.8121 (mp) REVERT: C 476 PHE cc_start: 0.7996 (m-80) cc_final: 0.7631 (m-80) REVERT: C 486 LYS cc_start: 0.6458 (mtpp) cc_final: 0.6123 (mtpp) REVERT: C 503 MET cc_start: 0.8225 (tpp) cc_final: 0.7760 (tpp) REVERT: C 504 GLU cc_start: 0.8422 (tp30) cc_final: 0.8185 (tp30) REVERT: C 524 ARG cc_start: 0.7823 (mmt90) cc_final: 0.7556 (mmt90) REVERT: C 566 LYS cc_start: 0.8673 (pttp) cc_final: 0.8256 (pttp) REVERT: C 582 LEU cc_start: 0.9000 (mt) cc_final: 0.8767 (mt) REVERT: D 78 ASN cc_start: 0.8674 (t0) cc_final: 0.8202 (t0) REVERT: D 160 LYS cc_start: 0.8775 (tmmt) cc_final: 0.8551 (tppt) outliers start: 2 outliers final: 0 residues processed: 469 average time/residue: 0.1215 time to fit residues: 78.8568 Evaluate side-chains 410 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 519 ASN A 523 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN C 201 GLN C 319 GLN C 360 HIS C 573 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.154008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.120026 restraints weight = 30366.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124302 restraints weight = 17548.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127168 restraints weight = 11447.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.129174 restraints weight = 8190.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130648 restraints weight = 6293.329| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14205 Z= 0.244 Angle : 0.765 10.675 19562 Z= 0.417 Chirality : 0.047 0.208 2195 Planarity : 0.005 0.061 2244 Dihedral : 21.208 164.924 2554 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.25 % Favored : 90.68 % Rotamer: Outliers : 0.52 % Allowed : 6.52 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.21), residues: 1535 helix: -0.42 (0.20), residues: 596 sheet: -0.48 (0.37), residues: 222 loop : -2.02 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 77 TYR 0.023 0.002 TYR A 595 PHE 0.029 0.002 PHE A 589 TRP 0.037 0.003 TRP C 406 HIS 0.014 0.002 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.24 (14204) covalent geometry : angle 0.76514 / 0.42 (19562) hydrogen bonds : bond 0.05806 / 3.89 ( 580) hydrogen bonds : angle 5.81460 / 4.14 ( 1605) Misc. bond : bond 0.00566 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 448 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9154 (mttt) cc_final: 0.8862 (mttp) REVERT: A 66 PHE cc_start: 0.7236 (m-80) cc_final: 0.6953 (m-80) REVERT: A 119 ASP cc_start: 0.8616 (p0) cc_final: 0.8378 (p0) REVERT: A 178 VAL cc_start: 0.8736 (p) cc_final: 0.8421 (p) REVERT: A 181 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.8161 (ttp80) REVERT: A 222 LEU cc_start: 0.8769 (tp) cc_final: 0.8512 (tp) REVERT: A 231 LYS cc_start: 0.8991 (mptt) cc_final: 0.8685 (mptt) REVERT: A 236 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8668 (tppt) REVERT: A 255 LEU cc_start: 0.7812 (mt) cc_final: 0.7407 (mm) REVERT: A 260 ASP cc_start: 0.7728 (p0) cc_final: 0.7472 (p0) REVERT: A 271 GLN cc_start: 0.8545 (tp-100) cc_final: 0.8108 (tp-100) REVERT: A 293 LYS cc_start: 0.7975 (pttm) cc_final: 0.7301 (pttm) REVERT: A 351 LYS cc_start: 0.8679 (tttp) cc_final: 0.8251 (tppt) REVERT: A 360 HIS cc_start: 0.8015 (t-90) cc_final: 0.7606 (t-90) REVERT: A 368 LYS cc_start: 0.8833 (mtpt) cc_final: 0.8502 (mtpt) REVERT: A 370 LEU cc_start: 0.8900 (tt) cc_final: 0.8695 (tt) REVERT: A 379 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7425 (mtp85) REVERT: A 380 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8072 (ttmt) REVERT: A 382 HIS cc_start: 0.7338 (t-90) cc_final: 0.7124 (t-90) REVERT: A 406 TRP cc_start: 0.8915 (t60) cc_final: 0.8610 (t60) REVERT: A 409 TYR cc_start: 0.8613 (t80) cc_final: 0.8231 (t80) REVERT: A 426 TYR cc_start: 0.7094 (p90) cc_final: 0.6601 (p90) REVERT: A 456 MET cc_start: 0.8197 (mtm) cc_final: 0.7986 (mtm) REVERT: A 489 ASN cc_start: 0.7270 (p0) cc_final: 0.6909 (p0) REVERT: A 505 LYS cc_start: 0.9306 (tmtt) cc_final: 0.8905 (tmtt) REVERT: A 516 VAL cc_start: 0.8881 (m) cc_final: 0.8250 (p) REVERT: A 520 ASN cc_start: 0.8671 (m-40) cc_final: 0.8298 (m-40) REVERT: A 525 ASN cc_start: 0.6944 (m-40) cc_final: 0.6411 (m110) REVERT: A 526 TYR cc_start: 0.6965 (m-10) cc_final: 0.6255 (m-80) REVERT: A 565 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7696 (mt-10) REVERT: B 1 MET cc_start: 0.6508 (ptt) cc_final: 0.6289 (ptt) REVERT: C 6 MET cc_start: 0.7444 (ptm) cc_final: 0.7239 (ptm) REVERT: C 53 LYS cc_start: 0.7745 (mppt) cc_final: 0.6906 (mppt) REVERT: C 95 LYS cc_start: 0.9103 (mppt) cc_final: 0.8615 (mppt) REVERT: C 128 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7050 (mt-10) REVERT: C 137 MET cc_start: 0.7722 (ptp) cc_final: 0.7502 (ptp) REVERT: C 139 LYS cc_start: 0.7285 (tmmt) cc_final: 0.6831 (tttm) REVERT: C 144 GLU cc_start: 0.7071 (tp30) cc_final: 0.6788 (tp30) REVERT: C 199 TYR cc_start: 0.8188 (t80) cc_final: 0.7983 (t80) REVERT: C 204 TYR cc_start: 0.7676 (m-80) cc_final: 0.7376 (m-10) REVERT: C 232 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7751 (mp) REVERT: C 236 LYS cc_start: 0.8699 (mppt) cc_final: 0.8091 (mppt) REVERT: C 244 GLN cc_start: 0.6034 (tp-100) cc_final: 0.5718 (tp40) REVERT: C 251 LYS cc_start: 0.7736 (tmtt) cc_final: 0.7498 (tmtt) REVERT: C 301 LEU cc_start: 0.8384 (tp) cc_final: 0.8036 (tp) REVERT: C 302 ASN cc_start: 0.8302 (t0) cc_final: 0.7959 (m-40) REVERT: C 308 ARG cc_start: 0.8759 (ttp-170) cc_final: 0.8494 (ttm-80) REVERT: C 323 GLN cc_start: 0.8759 (mt0) cc_final: 0.8532 (mm-40) REVERT: C 351 LYS cc_start: 0.8962 (ttmm) cc_final: 0.8724 (tmtt) REVERT: C 357 GLN cc_start: 0.8115 (tt0) cc_final: 0.7296 (tt0) REVERT: C 365 ASP cc_start: 0.8087 (p0) cc_final: 0.7776 (p0) REVERT: C 368 LYS cc_start: 0.9113 (ttmm) cc_final: 0.8857 (ttmm) REVERT: C 398 GLU cc_start: 0.7934 (tt0) cc_final: 0.7028 (tt0) REVERT: C 438 GLU cc_start: 0.7965 (mm-30) cc_final: 0.6875 (tp30) REVERT: C 442 CYS cc_start: 0.6736 (p) cc_final: 0.6511 (m) REVERT: C 476 PHE cc_start: 0.7898 (m-80) cc_final: 0.7576 (m-80) REVERT: C 503 MET cc_start: 0.8426 (tpp) cc_final: 0.8095 (tpp) REVERT: C 504 GLU cc_start: 0.8616 (tp30) cc_final: 0.8215 (tp30) REVERT: C 557 LEU cc_start: 0.8895 (mm) cc_final: 0.8553 (mm) REVERT: C 566 LYS cc_start: 0.8715 (pttp) cc_final: 0.8308 (pttp) REVERT: C 584 HIS cc_start: 0.8447 (m90) cc_final: 0.8118 (m90) REVERT: C 590 LYS cc_start: 0.8533 (tttt) cc_final: 0.8177 (tttt) REVERT: C 606 LEU cc_start: 0.8703 (mp) cc_final: 0.8471 (mp) REVERT: D 18 ASP cc_start: 0.6191 (m-30) cc_final: 0.5904 (m-30) REVERT: D 78 ASN cc_start: 0.9062 (t0) cc_final: 0.8646 (t0) REVERT: D 99 MET cc_start: 0.6976 (ttm) cc_final: 0.6347 (ttm) REVERT: D 140 LEU cc_start: 0.8978 (tt) cc_final: 0.8772 (tt) outliers start: 7 outliers final: 1 residues processed: 451 average time/residue: 0.1122 time to fit residues: 71.1292 Evaluate side-chains 404 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 402 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 47 optimal weight: 0.3980 chunk 158 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 182 GLN C 319 GLN C 415 HIS C 594 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.155265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.121292 restraints weight = 30266.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125608 restraints weight = 17354.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.128591 restraints weight = 11316.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.130595 restraints weight = 8047.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.132141 restraints weight = 6185.137| |-----------------------------------------------------------------------------| r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14205 Z= 0.156 Angle : 0.715 11.167 19562 Z= 0.380 Chirality : 0.044 0.189 2195 Planarity : 0.005 0.091 2244 Dihedral : 21.253 162.845 2554 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.79 % Favored : 91.14 % Rotamer: Outliers : 0.30 % Allowed : 4.34 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.21), residues: 1535 helix: -0.23 (0.21), residues: 588 sheet: -0.52 (0.37), residues: 219 loop : -1.87 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 434 TYR 0.024 0.002 TYR C 411 PHE 0.035 0.002 PHE A 589 TRP 0.024 0.001 TRP C 406 HIS 0.010 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.16 (14204) covalent geometry : angle 0.71513 / 0.38 (19562) hydrogen bonds : bond 0.05079 / 3.36 ( 580) hydrogen bonds : angle 5.53376 / 3.96 ( 1605) Misc. bond : bond 0.00136 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 430 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9109 (mttt) cc_final: 0.8459 (mttp) REVERT: A 3 THR cc_start: 0.8745 (t) cc_final: 0.5782 (t) REVERT: A 66 PHE cc_start: 0.7178 (m-80) cc_final: 0.6930 (m-80) REVERT: A 119 ASP cc_start: 0.8633 (p0) cc_final: 0.8397 (p0) REVERT: A 226 VAL cc_start: 0.8700 (p) cc_final: 0.8438 (p) REVERT: A 231 LYS cc_start: 0.8930 (mptt) cc_final: 0.8648 (mptt) REVERT: A 255 LEU cc_start: 0.7720 (mt) cc_final: 0.7324 (mm) REVERT: A 260 ASP cc_start: 0.7754 (p0) cc_final: 0.7517 (p0) REVERT: A 272 MET cc_start: 0.7812 (mtt) cc_final: 0.7321 (mtt) REVERT: A 290 ARG cc_start: 0.8461 (ppt170) cc_final: 0.7904 (ppt170) REVERT: A 293 LYS cc_start: 0.7947 (pttm) cc_final: 0.7260 (pttm) REVERT: A 305 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8214 (tp30) REVERT: A 316 MET cc_start: 0.7018 (tmm) cc_final: 0.6506 (tmm) REVERT: A 320 HIS cc_start: 0.6970 (t-90) cc_final: 0.6591 (t-90) REVERT: A 346 GLU cc_start: 0.7705 (mp0) cc_final: 0.7365 (mp0) REVERT: A 351 LYS cc_start: 0.8597 (tttp) cc_final: 0.7768 (mmtm) REVERT: A 360 HIS cc_start: 0.8095 (t-90) cc_final: 0.7608 (t-90) REVERT: A 366 THR cc_start: 0.8603 (p) cc_final: 0.8391 (p) REVERT: A 368 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8484 (mtpt) REVERT: A 369 ARG cc_start: 0.9053 (ptm-80) cc_final: 0.8669 (ptm-80) REVERT: A 370 LEU cc_start: 0.8881 (tt) cc_final: 0.8417 (tt) REVERT: A 379 ARG cc_start: 0.7709 (mtp85) cc_final: 0.7464 (mtp85) REVERT: A 380 LYS cc_start: 0.8319 (ttpt) cc_final: 0.8066 (ttmt) REVERT: A 406 TRP cc_start: 0.8814 (t60) cc_final: 0.8489 (t60) REVERT: A 409 TYR cc_start: 0.8620 (t80) cc_final: 0.8207 (t80) REVERT: A 426 TYR cc_start: 0.7100 (p90) cc_final: 0.6612 (p90) REVERT: A 430 THR cc_start: 0.8240 (m) cc_final: 0.7996 (p) REVERT: A 456 MET cc_start: 0.8209 (mtm) cc_final: 0.7950 (mtm) REVERT: A 489 ASN cc_start: 0.7169 (p0) cc_final: 0.6795 (p0) REVERT: A 505 LYS cc_start: 0.9278 (tmtt) cc_final: 0.8861 (tmtt) REVERT: A 516 VAL cc_start: 0.8879 (m) cc_final: 0.8238 (p) REVERT: A 519 ASN cc_start: 0.7964 (m110) cc_final: 0.7645 (m110) REVERT: A 520 ASN cc_start: 0.8696 (m-40) cc_final: 0.8330 (m-40) REVERT: A 525 ASN cc_start: 0.6915 (m-40) cc_final: 0.6318 (m110) REVERT: A 565 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 569 ASN cc_start: 0.7047 (m110) cc_final: 0.6743 (m110) REVERT: B 136 LYS cc_start: 0.7539 (mmpt) cc_final: 0.6867 (mmpt) REVERT: B 143 ASN cc_start: 0.8215 (p0) cc_final: 0.7872 (p0) REVERT: C 15 GLN cc_start: 0.8358 (pp30) cc_final: 0.8126 (pp30) REVERT: C 32 LEU cc_start: 0.7907 (mt) cc_final: 0.7697 (mt) REVERT: C 53 LYS cc_start: 0.7647 (mppt) cc_final: 0.6783 (mppt) REVERT: C 71 ASN cc_start: 0.7613 (m110) cc_final: 0.7383 (m110) REVERT: C 90 LYS cc_start: 0.8445 (ptmm) cc_final: 0.7973 (ptmm) REVERT: C 95 LYS cc_start: 0.9090 (mppt) cc_final: 0.8614 (mppt) REVERT: C 128 GLU cc_start: 0.7543 (mt-10) cc_final: 0.6982 (mt-10) REVERT: C 139 LYS cc_start: 0.7437 (tmmt) cc_final: 0.6988 (tttm) REVERT: C 144 GLU cc_start: 0.7019 (tp30) cc_final: 0.6725 (tp30) REVERT: C 169 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8149 (tm-30) REVERT: C 199 TYR cc_start: 0.7980 (t80) cc_final: 0.7664 (t80) REVERT: C 204 TYR cc_start: 0.7648 (m-80) cc_final: 0.7368 (m-10) REVERT: C 232 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7731 (mp) REVERT: C 236 LYS cc_start: 0.8665 (mppt) cc_final: 0.8060 (mppt) REVERT: C 244 GLN cc_start: 0.5977 (tp-100) cc_final: 0.5757 (tp40) REVERT: C 267 ARG cc_start: 0.8024 (ppt170) cc_final: 0.7636 (ppt170) REVERT: C 302 ASN cc_start: 0.8343 (t0) cc_final: 0.7999 (m-40) REVERT: C 323 GLN cc_start: 0.8741 (mt0) cc_final: 0.8457 (mm-40) REVERT: C 350 LEU cc_start: 0.8535 (mm) cc_final: 0.8298 (mm) REVERT: C 351 LYS cc_start: 0.8974 (ttmm) cc_final: 0.8671 (tmtt) REVERT: C 357 GLN cc_start: 0.7964 (tt0) cc_final: 0.7190 (tt0) REVERT: C 365 ASP cc_start: 0.7955 (p0) cc_final: 0.7695 (p0) REVERT: C 398 GLU cc_start: 0.8045 (tt0) cc_final: 0.6992 (tt0) REVERT: C 442 CYS cc_start: 0.6722 (p) cc_final: 0.6286 (m) REVERT: C 449 SER cc_start: 0.8654 (t) cc_final: 0.8431 (t) REVERT: C 454 GLU cc_start: 0.7938 (pt0) cc_final: 0.7710 (pt0) REVERT: C 476 PHE cc_start: 0.7910 (m-80) cc_final: 0.7619 (m-80) REVERT: C 503 MET cc_start: 0.8337 (tpp) cc_final: 0.7963 (tpp) REVERT: C 504 GLU cc_start: 0.8575 (tp30) cc_final: 0.8087 (tp30) REVERT: C 557 LEU cc_start: 0.8877 (mm) cc_final: 0.8539 (mm) REVERT: C 566 LYS cc_start: 0.8669 (pttp) cc_final: 0.8294 (pttp) REVERT: C 584 HIS cc_start: 0.8443 (m90) cc_final: 0.8092 (m90) REVERT: C 590 LYS cc_start: 0.8261 (tttt) cc_final: 0.7512 (tttt) REVERT: C 591 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7411 (mmm160) REVERT: C 606 LEU cc_start: 0.8696 (mp) cc_final: 0.8416 (mp) REVERT: D 18 ASP cc_start: 0.6132 (m-30) cc_final: 0.5898 (m-30) REVERT: D 78 ASN cc_start: 0.9042 (t0) cc_final: 0.8646 (t0) REVERT: D 99 MET cc_start: 0.6932 (ttm) cc_final: 0.6268 (ttm) REVERT: D 103 HIS cc_start: 0.6475 (m-70) cc_final: 0.6131 (m90) REVERT: D 140 LEU cc_start: 0.8991 (tt) cc_final: 0.8760 (tt) REVERT: D 157 LEU cc_start: 0.8633 (mm) cc_final: 0.8270 (mm) outliers start: 4 outliers final: 0 residues processed: 430 average time/residue: 0.1079 time to fit residues: 65.6384 Evaluate side-chains 396 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 395 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 157 optimal weight: 30.0000 chunk 97 optimal weight: 4.9990 chunk 44 optimal weight: 5.9990 chunk 87 optimal weight: 0.2980 chunk 55 optimal weight: 0.0010 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 248 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN C 360 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.157701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.123570 restraints weight = 30101.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127839 restraints weight = 17402.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130806 restraints weight = 11392.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132847 restraints weight = 8138.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.134290 restraints weight = 6242.045| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14205 Z= 0.147 Angle : 0.712 9.833 19562 Z= 0.381 Chirality : 0.044 0.190 2195 Planarity : 0.005 0.071 2244 Dihedral : 21.292 161.677 2554 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.73 % Favored : 91.21 % Rotamer: Outliers : 0.07 % Allowed : 3.82 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.21), residues: 1535 helix: -0.18 (0.21), residues: 589 sheet: -0.48 (0.37), residues: 222 loop : -1.79 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 308 TYR 0.027 0.002 TYR A 41 PHE 0.067 0.002 PHE A 589 TRP 0.039 0.002 TRP C 406 HIS 0.012 0.001 HIS C 360 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (14204) covalent geometry : angle 0.71157 / 0.38 (19562) hydrogen bonds : bond 0.04988 / 3.32 ( 580) hydrogen bonds : angle 5.49690 / 3.91 ( 1605) Misc. bond : bond 0.00113 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7830 (tpt) cc_final: 0.7300 (tpt) REVERT: A 2 LYS cc_start: 0.9079 (mttt) cc_final: 0.8655 (mttp) REVERT: A 51 ARG cc_start: 0.8202 (pmt170) cc_final: 0.7261 (ptp90) REVERT: A 66 PHE cc_start: 0.7165 (m-80) cc_final: 0.6875 (m-80) REVERT: A 119 ASP cc_start: 0.8709 (p0) cc_final: 0.8461 (p0) REVERT: A 160 ILE cc_start: 0.8043 (pt) cc_final: 0.7666 (pt) REVERT: A 164 MET cc_start: 0.9092 (ptp) cc_final: 0.8824 (ptp) REVERT: A 226 VAL cc_start: 0.8734 (p) cc_final: 0.8406 (p) REVERT: A 228 ARG cc_start: 0.7917 (ttp-170) cc_final: 0.7675 (mtm180) REVERT: A 231 LYS cc_start: 0.8943 (mptt) cc_final: 0.8655 (mptt) REVERT: A 236 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8622 (tppt) REVERT: A 255 LEU cc_start: 0.7709 (mt) cc_final: 0.7345 (mm) REVERT: A 260 ASP cc_start: 0.7743 (p0) cc_final: 0.7514 (p0) REVERT: A 272 MET cc_start: 0.7712 (mtt) cc_final: 0.7218 (mtt) REVERT: A 290 ARG cc_start: 0.8428 (ppt170) cc_final: 0.8057 (pmt-80) REVERT: A 293 LYS cc_start: 0.7944 (pttm) cc_final: 0.7251 (pttm) REVERT: A 303 THR cc_start: 0.8296 (m) cc_final: 0.8017 (p) REVERT: A 305 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8201 (tp30) REVERT: A 316 MET cc_start: 0.6886 (tmm) cc_final: 0.6623 (tmm) REVERT: A 320 HIS cc_start: 0.7166 (t-90) cc_final: 0.6865 (t-90) REVERT: A 346 GLU cc_start: 0.7721 (mp0) cc_final: 0.7357 (mp0) REVERT: A 366 THR cc_start: 0.8588 (p) cc_final: 0.8343 (p) REVERT: A 368 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8464 (mtpt) REVERT: A 369 ARG cc_start: 0.9057 (ptm-80) cc_final: 0.8651 (ptm-80) REVERT: A 370 LEU cc_start: 0.8866 (tt) cc_final: 0.8407 (tt) REVERT: A 379 ARG cc_start: 0.7720 (mtp85) cc_final: 0.7293 (mtp85) REVERT: A 380 LYS cc_start: 0.8342 (ttpt) cc_final: 0.8057 (ttmt) REVERT: A 382 HIS cc_start: 0.7217 (t-90) cc_final: 0.7016 (t-90) REVERT: A 406 TRP cc_start: 0.8823 (t60) cc_final: 0.8435 (t60) REVERT: A 409 TYR cc_start: 0.8613 (t80) cc_final: 0.8213 (t80) REVERT: A 426 TYR cc_start: 0.7098 (p90) cc_final: 0.6633 (p90) REVERT: A 430 THR cc_start: 0.8198 (m) cc_final: 0.7984 (p) REVERT: A 489 ASN cc_start: 0.7217 (p0) cc_final: 0.6940 (p0) REVERT: A 505 LYS cc_start: 0.9239 (tmtt) cc_final: 0.8850 (tmtt) REVERT: A 516 VAL cc_start: 0.8877 (m) cc_final: 0.8257 (p) REVERT: A 520 ASN cc_start: 0.8718 (m-40) cc_final: 0.8331 (m-40) REVERT: A 525 ASN cc_start: 0.6979 (m-40) cc_final: 0.6382 (m110) REVERT: A 565 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 569 ASN cc_start: 0.6956 (m110) cc_final: 0.6661 (m110) REVERT: A 603 MET cc_start: 0.8466 (mtm) cc_final: 0.8238 (mtm) REVERT: B 71 LEU cc_start: 0.7957 (mt) cc_final: 0.7724 (mt) REVERT: B 136 LYS cc_start: 0.7834 (mmpt) cc_final: 0.7105 (mmpt) REVERT: B 154 VAL cc_start: 0.8327 (p) cc_final: 0.7964 (p) REVERT: C 15 GLN cc_start: 0.8387 (pp30) cc_final: 0.8168 (pp30) REVERT: C 53 LYS cc_start: 0.7480 (mppt) cc_final: 0.6666 (tppt) REVERT: C 71 ASN cc_start: 0.7630 (m110) cc_final: 0.7385 (m110) REVERT: C 95 LYS cc_start: 0.9101 (mppt) cc_final: 0.8669 (mppt) REVERT: C 128 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6919 (mt-10) REVERT: C 139 LYS cc_start: 0.7429 (tmmt) cc_final: 0.6961 (ptmm) REVERT: C 144 GLU cc_start: 0.7006 (tp30) cc_final: 0.6703 (tp30) REVERT: C 164 MET cc_start: 0.8492 (ppp) cc_final: 0.8121 (ppp) REVERT: C 169 GLU cc_start: 0.8379 (tm-30) cc_final: 0.8051 (tm-30) REVERT: C 199 TYR cc_start: 0.7938 (t80) cc_final: 0.7633 (t80) REVERT: C 204 TYR cc_start: 0.7667 (m-80) cc_final: 0.7395 (m-10) REVERT: C 225 CYS cc_start: 0.8560 (m) cc_final: 0.8360 (m) REVERT: C 236 LYS cc_start: 0.8648 (mppt) cc_final: 0.8055 (mppt) REVERT: C 244 GLN cc_start: 0.6007 (tp-100) cc_final: 0.5718 (tp40) REVERT: C 267 ARG cc_start: 0.8003 (ppt170) cc_final: 0.7627 (ppt170) REVERT: C 292 GLU cc_start: 0.8628 (pm20) cc_final: 0.8225 (pm20) REVERT: C 302 ASN cc_start: 0.8307 (t0) cc_final: 0.8037 (m-40) REVERT: C 308 ARG cc_start: 0.8862 (ttp-170) cc_final: 0.8482 (tpp80) REVERT: C 323 GLN cc_start: 0.8738 (mt0) cc_final: 0.8405 (mm110) REVERT: C 350 LEU cc_start: 0.8623 (mm) cc_final: 0.8387 (mm) REVERT: C 351 LYS cc_start: 0.8960 (ttmm) cc_final: 0.8559 (tttm) REVERT: C 357 GLN cc_start: 0.7920 (tt0) cc_final: 0.7257 (tt0) REVERT: C 365 ASP cc_start: 0.7854 (p0) cc_final: 0.7642 (p0) REVERT: C 398 GLU cc_start: 0.7986 (tt0) cc_final: 0.7357 (tt0) REVERT: C 442 CYS cc_start: 0.6665 (p) cc_final: 0.6202 (m) REVERT: C 464 GLU cc_start: 0.7100 (mp0) cc_final: 0.6845 (mp0) REVERT: C 476 PHE cc_start: 0.7942 (m-80) cc_final: 0.7672 (m-80) REVERT: C 499 LEU cc_start: 0.8544 (tp) cc_final: 0.8296 (tt) REVERT: C 503 MET cc_start: 0.8212 (tpp) cc_final: 0.7849 (tpp) REVERT: C 504 GLU cc_start: 0.8521 (tp30) cc_final: 0.8068 (tp30) REVERT: C 550 LYS cc_start: 0.8272 (mttt) cc_final: 0.8030 (mttt) REVERT: C 557 LEU cc_start: 0.8916 (mm) cc_final: 0.8567 (mm) REVERT: C 566 LYS cc_start: 0.8677 (pttp) cc_final: 0.8284 (pttp) REVERT: C 582 LEU cc_start: 0.8873 (mt) cc_final: 0.8391 (mt) REVERT: C 584 HIS cc_start: 0.8458 (m90) cc_final: 0.8127 (m90) REVERT: C 606 LEU cc_start: 0.8685 (mp) cc_final: 0.8397 (mp) REVERT: D 18 ASP cc_start: 0.6148 (m-30) cc_final: 0.5749 (m-30) REVERT: D 78 ASN cc_start: 0.9001 (t0) cc_final: 0.8575 (t0) REVERT: D 103 HIS cc_start: 0.6570 (m-70) cc_final: 0.6264 (m90) REVERT: D 140 LEU cc_start: 0.8988 (tt) cc_final: 0.8760 (tt) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.1052 time to fit residues: 66.2056 Evaluate side-chains 385 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 93 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 0.0870 chunk 84 optimal weight: 0.0030 overall best weight: 0.3568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.157621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123095 restraints weight = 30163.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.127575 restraints weight = 17246.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.130532 restraints weight = 11200.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.132650 restraints weight = 7985.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.134201 restraints weight = 6074.132| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14205 Z= 0.140 Angle : 0.693 11.057 19562 Z= 0.368 Chirality : 0.043 0.190 2195 Planarity : 0.005 0.067 2244 Dihedral : 21.307 160.744 2554 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.21), residues: 1535 helix: -0.04 (0.21), residues: 589 sheet: -0.57 (0.37), residues: 226 loop : -1.73 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 308 TYR 0.027 0.002 TYR A 41 PHE 0.035 0.002 PHE A 192 TRP 0.021 0.001 TRP C 406 HIS 0.009 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (14204) covalent geometry : angle 0.69266 / 0.37 (19562) hydrogen bonds : bond 0.04697 / 3.10 ( 580) hydrogen bonds : angle 5.32551 / 3.79 ( 1605) Misc. bond : bond 0.00099 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7930 (tpt) cc_final: 0.7445 (tpt) REVERT: A 2 LYS cc_start: 0.9069 (mttt) cc_final: 0.8805 (mmtp) REVERT: A 51 ARG cc_start: 0.8180 (pmt170) cc_final: 0.7532 (ptp90) REVERT: A 65 ASP cc_start: 0.8587 (t70) cc_final: 0.8245 (t0) REVERT: A 66 PHE cc_start: 0.7230 (m-80) cc_final: 0.6930 (m-80) REVERT: A 119 ASP cc_start: 0.8658 (p0) cc_final: 0.8432 (p0) REVERT: A 226 VAL cc_start: 0.8725 (p) cc_final: 0.8376 (p) REVERT: A 228 ARG cc_start: 0.8002 (ttp-170) cc_final: 0.7600 (ttp80) REVERT: A 231 LYS cc_start: 0.8956 (mptt) cc_final: 0.8697 (mptt) REVERT: A 255 LEU cc_start: 0.7710 (mt) cc_final: 0.7324 (mm) REVERT: A 260 ASP cc_start: 0.7779 (p0) cc_final: 0.7556 (p0) REVERT: A 272 MET cc_start: 0.7667 (mtt) cc_final: 0.7285 (mtt) REVERT: A 290 ARG cc_start: 0.8446 (ppt170) cc_final: 0.8063 (pmt-80) REVERT: A 293 LYS cc_start: 0.7951 (pttm) cc_final: 0.7262 (pttm) REVERT: A 297 ARG cc_start: 0.6066 (ptm160) cc_final: 0.5846 (ptm160) REVERT: A 305 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8129 (tp30) REVERT: A 316 MET cc_start: 0.6934 (tmm) cc_final: 0.6682 (tmm) REVERT: A 320 HIS cc_start: 0.7272 (t-90) cc_final: 0.6759 (t-90) REVERT: A 346 GLU cc_start: 0.7741 (mp0) cc_final: 0.7391 (mp0) REVERT: A 366 THR cc_start: 0.8568 (p) cc_final: 0.8302 (p) REVERT: A 368 LYS cc_start: 0.8817 (mtpt) cc_final: 0.8460 (mtpt) REVERT: A 369 ARG cc_start: 0.9049 (ptm-80) cc_final: 0.8633 (ptm-80) REVERT: A 370 LEU cc_start: 0.8853 (tt) cc_final: 0.8374 (tt) REVERT: A 379 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7448 (mtp85) REVERT: A 380 LYS cc_start: 0.8367 (ttpt) cc_final: 0.8160 (ttmt) REVERT: A 406 TRP cc_start: 0.8819 (t60) cc_final: 0.8304 (t60) REVERT: A 409 TYR cc_start: 0.8638 (t80) cc_final: 0.8260 (t80) REVERT: A 426 TYR cc_start: 0.7056 (p90) cc_final: 0.6584 (p90) REVERT: A 430 THR cc_start: 0.8175 (m) cc_final: 0.7950 (p) REVERT: A 486 LYS cc_start: 0.8304 (tmmt) cc_final: 0.8028 (ttpp) REVERT: A 489 ASN cc_start: 0.7096 (p0) cc_final: 0.6786 (p0) REVERT: A 505 LYS cc_start: 0.9231 (tmtt) cc_final: 0.8856 (tmtt) REVERT: A 516 VAL cc_start: 0.8871 (m) cc_final: 0.8260 (p) REVERT: A 520 ASN cc_start: 0.8735 (m-40) cc_final: 0.8340 (m-40) REVERT: A 525 ASN cc_start: 0.6835 (m-40) cc_final: 0.6198 (m110) REVERT: A 565 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 569 ASN cc_start: 0.6965 (m110) cc_final: 0.6685 (m110) REVERT: A 603 MET cc_start: 0.8504 (mtm) cc_final: 0.8220 (mtm) REVERT: B 136 LYS cc_start: 0.7751 (mmpt) cc_final: 0.7067 (mmpt) REVERT: C 32 LEU cc_start: 0.7909 (mt) cc_final: 0.7660 (mt) REVERT: C 53 LYS cc_start: 0.7434 (mppt) cc_final: 0.6647 (tppt) REVERT: C 95 LYS cc_start: 0.9088 (mppt) cc_final: 0.8637 (mppt) REVERT: C 98 MET cc_start: 0.7328 (ttt) cc_final: 0.6862 (ttt) REVERT: C 128 GLU cc_start: 0.7452 (mt-10) cc_final: 0.6902 (mt-10) REVERT: C 139 LYS cc_start: 0.7417 (tmmt) cc_final: 0.7021 (ptmm) REVERT: C 144 GLU cc_start: 0.7067 (tp30) cc_final: 0.6795 (tp30) REVERT: C 164 MET cc_start: 0.8516 (ppp) cc_final: 0.8199 (ppp) REVERT: C 169 GLU cc_start: 0.8400 (tm-30) cc_final: 0.8047 (tm-30) REVERT: C 199 TYR cc_start: 0.7864 (t80) cc_final: 0.7599 (t80) REVERT: C 204 TYR cc_start: 0.7674 (m-80) cc_final: 0.7396 (m-10) REVERT: C 236 LYS cc_start: 0.8661 (mppt) cc_final: 0.8069 (mppt) REVERT: C 244 GLN cc_start: 0.5962 (tp-100) cc_final: 0.5660 (tp40) REVERT: C 263 ARG cc_start: 0.8307 (ptt180) cc_final: 0.6815 (ptt180) REVERT: C 267 ARG cc_start: 0.8012 (ppt170) cc_final: 0.7648 (ppt170) REVERT: C 302 ASN cc_start: 0.8310 (t0) cc_final: 0.7995 (m-40) REVERT: C 306 MET cc_start: 0.7952 (tmm) cc_final: 0.7315 (tmm) REVERT: C 323 GLN cc_start: 0.8741 (mt0) cc_final: 0.8393 (mm110) REVERT: C 351 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8648 (tttm) REVERT: C 357 GLN cc_start: 0.7948 (tt0) cc_final: 0.7329 (tt0) REVERT: C 365 ASP cc_start: 0.7811 (p0) cc_final: 0.7535 (p0) REVERT: C 398 GLU cc_start: 0.8073 (tt0) cc_final: 0.7484 (tt0) REVERT: C 442 CYS cc_start: 0.6644 (p) cc_final: 0.6182 (m) REVERT: C 449 SER cc_start: 0.8637 (t) cc_final: 0.8431 (t) REVERT: C 464 GLU cc_start: 0.7091 (mp0) cc_final: 0.6845 (mp0) REVERT: C 476 PHE cc_start: 0.7925 (m-80) cc_final: 0.7656 (m-80) REVERT: C 503 MET cc_start: 0.8283 (tpp) cc_final: 0.7849 (tpp) REVERT: C 504 GLU cc_start: 0.8538 (tp30) cc_final: 0.8089 (tp30) REVERT: C 550 LYS cc_start: 0.8324 (mttt) cc_final: 0.8090 (mttt) REVERT: C 557 LEU cc_start: 0.8893 (mm) cc_final: 0.8532 (mm) REVERT: C 566 LYS cc_start: 0.8670 (pttp) cc_final: 0.8272 (pttp) REVERT: C 582 LEU cc_start: 0.8814 (mt) cc_final: 0.8340 (mt) REVERT: C 584 HIS cc_start: 0.8458 (m90) cc_final: 0.8132 (m90) REVERT: C 606 LEU cc_start: 0.8700 (mp) cc_final: 0.8417 (mp) REVERT: D 78 ASN cc_start: 0.8967 (t0) cc_final: 0.8217 (t0) REVERT: D 103 HIS cc_start: 0.6724 (m-70) cc_final: 0.6433 (m-70) REVERT: D 140 LEU cc_start: 0.8986 (tt) cc_final: 0.8761 (tt) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.1134 time to fit residues: 71.4950 Evaluate side-chains 400 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 138 optimal weight: 0.2980 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 201 GLN C 356 GLN C 360 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.157050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122580 restraints weight = 30087.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.126972 restraints weight = 17167.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130017 restraints weight = 11166.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.132040 restraints weight = 7919.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.133585 restraints weight = 6065.798| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14205 Z= 0.145 Angle : 0.706 10.185 19562 Z= 0.374 Chirality : 0.044 0.196 2195 Planarity : 0.005 0.071 2244 Dihedral : 21.338 160.405 2554 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.21), residues: 1535 helix: -0.04 (0.21), residues: 588 sheet: -0.57 (0.36), residues: 226 loop : -1.74 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 472 TYR 0.032 0.002 TYR A 41 PHE 0.064 0.002 PHE A 589 TRP 0.031 0.002 TRP C 406 HIS 0.010 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (14204) covalent geometry : angle 0.70585 / 0.37 (19562) hydrogen bonds : bond 0.04642 / 3.05 ( 580) hydrogen bonds : angle 5.32392 / 3.79 ( 1605) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 451 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8195 (pmt170) cc_final: 0.7419 (ptp90) REVERT: A 65 ASP cc_start: 0.8603 (t70) cc_final: 0.8272 (t0) REVERT: A 66 PHE cc_start: 0.7284 (m-80) cc_final: 0.6965 (m-80) REVERT: A 119 ASP cc_start: 0.8711 (p0) cc_final: 0.8503 (p0) REVERT: A 226 VAL cc_start: 0.8733 (p) cc_final: 0.8370 (p) REVERT: A 231 LYS cc_start: 0.8964 (mptt) cc_final: 0.8696 (mptt) REVERT: A 236 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8592 (tppt) REVERT: A 246 LYS cc_start: 0.7808 (pptt) cc_final: 0.7025 (tmtt) REVERT: A 255 LEU cc_start: 0.7738 (mt) cc_final: 0.7366 (mm) REVERT: A 260 ASP cc_start: 0.7810 (p0) cc_final: 0.7480 (p0) REVERT: A 272 MET cc_start: 0.7694 (mtt) cc_final: 0.7302 (mtt) REVERT: A 290 ARG cc_start: 0.8453 (ppt170) cc_final: 0.8086 (pmt-80) REVERT: A 293 LYS cc_start: 0.7980 (pttm) cc_final: 0.7290 (pttm) REVERT: A 305 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8190 (tp30) REVERT: A 346 GLU cc_start: 0.7790 (mp0) cc_final: 0.7463 (mp0) REVERT: A 351 LYS cc_start: 0.8680 (tppt) cc_final: 0.8020 (mmtm) REVERT: A 366 THR cc_start: 0.8551 (p) cc_final: 0.8299 (p) REVERT: A 368 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8476 (mtpt) REVERT: A 369 ARG cc_start: 0.9061 (ptm-80) cc_final: 0.8657 (ptm-80) REVERT: A 370 LEU cc_start: 0.8873 (tt) cc_final: 0.8384 (tt) REVERT: A 379 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7451 (mtp85) REVERT: A 398 GLU cc_start: 0.7435 (pm20) cc_final: 0.7216 (pm20) REVERT: A 409 TYR cc_start: 0.8658 (t80) cc_final: 0.8313 (t80) REVERT: A 426 TYR cc_start: 0.7066 (p90) cc_final: 0.6628 (p90) REVERT: A 482 LYS cc_start: 0.7757 (mmmm) cc_final: 0.7054 (mmmm) REVERT: A 489 ASN cc_start: 0.7083 (p0) cc_final: 0.6796 (p0) REVERT: A 502 LEU cc_start: 0.9059 (pp) cc_final: 0.8609 (pp) REVERT: A 516 VAL cc_start: 0.8847 (m) cc_final: 0.8261 (p) REVERT: A 520 ASN cc_start: 0.8787 (m-40) cc_final: 0.8388 (m-40) REVERT: A 525 ASN cc_start: 0.6931 (m-40) cc_final: 0.6345 (m110) REVERT: A 560 ILE cc_start: 0.8170 (mt) cc_final: 0.7927 (pt) REVERT: A 565 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 569 ASN cc_start: 0.7071 (m110) cc_final: 0.6682 (m110) REVERT: A 603 MET cc_start: 0.8537 (mtm) cc_final: 0.8241 (mtm) REVERT: B 136 LYS cc_start: 0.7858 (mmpt) cc_final: 0.7125 (mmpt) REVERT: C 15 GLN cc_start: 0.8376 (pp30) cc_final: 0.8176 (pp30) REVERT: C 32 LEU cc_start: 0.7945 (mt) cc_final: 0.7694 (mt) REVERT: C 41 TYR cc_start: 0.7027 (p90) cc_final: 0.6787 (p90) REVERT: C 53 LYS cc_start: 0.7366 (mppt) cc_final: 0.6570 (tppt) REVERT: C 89 LYS cc_start: 0.8209 (mptt) cc_final: 0.7965 (mmtm) REVERT: C 95 LYS cc_start: 0.9080 (mppt) cc_final: 0.8627 (mppt) REVERT: C 98 MET cc_start: 0.7342 (ttt) cc_final: 0.6813 (ttt) REVERT: C 128 GLU cc_start: 0.7488 (mt-10) cc_final: 0.6951 (mt-10) REVERT: C 139 LYS cc_start: 0.7500 (tmmt) cc_final: 0.6649 (pttp) REVERT: C 144 GLU cc_start: 0.7099 (tp30) cc_final: 0.6827 (tp30) REVERT: C 159 ASP cc_start: 0.7641 (t0) cc_final: 0.7032 (t0) REVERT: C 164 MET cc_start: 0.8534 (ppp) cc_final: 0.8222 (ppp) REVERT: C 169 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8025 (tm-30) REVERT: C 199 TYR cc_start: 0.7892 (t80) cc_final: 0.7612 (t80) REVERT: C 204 TYR cc_start: 0.7717 (m-80) cc_final: 0.7403 (m-10) REVERT: C 236 LYS cc_start: 0.8683 (mppt) cc_final: 0.8092 (mppt) REVERT: C 244 GLN cc_start: 0.5976 (tp-100) cc_final: 0.5683 (tp40) REVERT: C 263 ARG cc_start: 0.8316 (ptt180) cc_final: 0.6797 (ptt180) REVERT: C 267 ARG cc_start: 0.8025 (ppt170) cc_final: 0.7693 (ppt170) REVERT: C 292 GLU cc_start: 0.8485 (pm20) cc_final: 0.8106 (pm20) REVERT: C 302 ASN cc_start: 0.8302 (t0) cc_final: 0.8008 (m-40) REVERT: C 306 MET cc_start: 0.7961 (tmm) cc_final: 0.7324 (tmm) REVERT: C 308 ARG cc_start: 0.8886 (ttp-170) cc_final: 0.8661 (ttm-80) REVERT: C 323 GLN cc_start: 0.8752 (mt0) cc_final: 0.8405 (mm110) REVERT: C 350 LEU cc_start: 0.8663 (mm) cc_final: 0.8447 (mm) REVERT: C 351 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8661 (tttm) REVERT: C 357 GLN cc_start: 0.7988 (tt0) cc_final: 0.7290 (tt0) REVERT: C 365 ASP cc_start: 0.7846 (p0) cc_final: 0.7546 (p0) REVERT: C 367 VAL cc_start: 0.8971 (t) cc_final: 0.8634 (p) REVERT: C 398 GLU cc_start: 0.8145 (tt0) cc_final: 0.7401 (tt0) REVERT: C 442 CYS cc_start: 0.6655 (p) cc_final: 0.6182 (m) REVERT: C 449 SER cc_start: 0.8654 (t) cc_final: 0.8428 (t) REVERT: C 464 GLU cc_start: 0.7085 (mp0) cc_final: 0.6719 (mp0) REVERT: C 476 PHE cc_start: 0.7959 (m-80) cc_final: 0.7710 (m-80) REVERT: C 504 GLU cc_start: 0.8530 (tp30) cc_final: 0.8116 (tp30) REVERT: C 550 LYS cc_start: 0.8343 (mttt) cc_final: 0.8112 (mttt) REVERT: C 557 LEU cc_start: 0.8866 (mm) cc_final: 0.8519 (mm) REVERT: C 566 LYS cc_start: 0.8672 (pttp) cc_final: 0.8279 (pttp) REVERT: C 582 LEU cc_start: 0.8878 (mt) cc_final: 0.8642 (mt) REVERT: C 584 HIS cc_start: 0.8497 (m90) cc_final: 0.8179 (m90) REVERT: C 606 LEU cc_start: 0.8693 (mp) cc_final: 0.8425 (mp) REVERT: D 18 ASP cc_start: 0.6155 (m-30) cc_final: 0.5446 (m-30) REVERT: D 78 ASN cc_start: 0.9002 (t0) cc_final: 0.8227 (t0) REVERT: D 103 HIS cc_start: 0.6807 (m-70) cc_final: 0.6559 (m-70) outliers start: 0 outliers final: 0 residues processed: 451 average time/residue: 0.1137 time to fit residues: 73.1251 Evaluate side-chains 408 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 51 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 133 optimal weight: 0.9990 chunk 102 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 356 GLN ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.156217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121801 restraints weight = 29859.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126174 restraints weight = 17223.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.129143 restraints weight = 11241.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.131328 restraints weight = 8037.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.132665 restraints weight = 6119.237| |-----------------------------------------------------------------------------| r_work (final): 0.3825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14205 Z= 0.149 Angle : 0.720 10.188 19562 Z= 0.378 Chirality : 0.044 0.191 2195 Planarity : 0.005 0.061 2244 Dihedral : 21.365 160.472 2554 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.21), residues: 1535 helix: -0.04 (0.21), residues: 591 sheet: -0.54 (0.36), residues: 232 loop : -1.74 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 46 TYR 0.030 0.002 TYR A 41 PHE 0.024 0.001 PHE A 192 TRP 0.037 0.002 TRP A 259 HIS 0.009 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (14204) covalent geometry : angle 0.72034 / 0.38 (19562) hydrogen bonds : bond 0.04590 / 3.00 ( 580) hydrogen bonds : angle 5.25348 / 3.73 ( 1605) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8606 (t70) cc_final: 0.8255 (t0) REVERT: A 66 PHE cc_start: 0.7116 (m-80) cc_final: 0.6838 (m-80) REVERT: A 119 ASP cc_start: 0.8755 (p0) cc_final: 0.8543 (p0) REVERT: A 181 ARG cc_start: 0.8638 (ttp80) cc_final: 0.7999 (ttp80) REVERT: A 231 LYS cc_start: 0.8966 (mptt) cc_final: 0.8699 (mptt) REVERT: A 255 LEU cc_start: 0.7747 (mt) cc_final: 0.7362 (mm) REVERT: A 272 MET cc_start: 0.7749 (mtt) cc_final: 0.7370 (mtt) REVERT: A 290 ARG cc_start: 0.8451 (ppt170) cc_final: 0.8066 (pmt-80) REVERT: A 293 LYS cc_start: 0.7976 (pttm) cc_final: 0.7297 (pttm) REVERT: A 297 ARG cc_start: 0.6110 (ptm160) cc_final: 0.5808 (ptm160) REVERT: A 305 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8207 (tp30) REVERT: A 346 GLU cc_start: 0.7805 (mp0) cc_final: 0.7470 (mp0) REVERT: A 366 THR cc_start: 0.8535 (p) cc_final: 0.8264 (p) REVERT: A 368 LYS cc_start: 0.8835 (mtpt) cc_final: 0.8477 (mtpt) REVERT: A 369 ARG cc_start: 0.9088 (ptm-80) cc_final: 0.8668 (ptm-80) REVERT: A 370 LEU cc_start: 0.8888 (tt) cc_final: 0.8459 (tt) REVERT: A 379 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7420 (mtp85) REVERT: A 382 HIS cc_start: 0.7151 (t-90) cc_final: 0.6930 (t-90) REVERT: A 398 GLU cc_start: 0.7453 (pm20) cc_final: 0.7165 (pm20) REVERT: A 409 TYR cc_start: 0.8672 (t80) cc_final: 0.8292 (t80) REVERT: A 426 TYR cc_start: 0.7057 (p90) cc_final: 0.6652 (p90) REVERT: A 482 LYS cc_start: 0.7838 (mmmm) cc_final: 0.7166 (mmmm) REVERT: A 489 ASN cc_start: 0.7034 (p0) cc_final: 0.6717 (p0) REVERT: A 502 LEU cc_start: 0.9062 (pp) cc_final: 0.8585 (pp) REVERT: A 516 VAL cc_start: 0.8823 (m) cc_final: 0.8256 (p) REVERT: A 518 ILE cc_start: 0.8921 (mm) cc_final: 0.8664 (tp) REVERT: A 520 ASN cc_start: 0.8739 (m-40) cc_final: 0.8295 (m-40) REVERT: A 525 ASN cc_start: 0.6921 (m-40) cc_final: 0.6323 (m110) REVERT: A 560 ILE cc_start: 0.8209 (mt) cc_final: 0.7929 (pt) REVERT: A 565 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 569 ASN cc_start: 0.7117 (m110) cc_final: 0.6761 (m110) REVERT: A 603 MET cc_start: 0.8487 (mtm) cc_final: 0.8224 (mtm) REVERT: B 136 LYS cc_start: 0.7772 (mmpt) cc_final: 0.7056 (mmpt) REVERT: C 32 LEU cc_start: 0.7942 (mt) cc_final: 0.7691 (mt) REVERT: C 53 LYS cc_start: 0.7335 (mppt) cc_final: 0.6581 (tppt) REVERT: C 71 ASN cc_start: 0.7815 (m-40) cc_final: 0.7562 (m110) REVERT: C 95 LYS cc_start: 0.9066 (mppt) cc_final: 0.8616 (mppt) REVERT: C 98 MET cc_start: 0.7381 (ttt) cc_final: 0.6863 (ttt) REVERT: C 128 GLU cc_start: 0.7473 (mt-10) cc_final: 0.6908 (mt-10) REVERT: C 139 LYS cc_start: 0.7475 (tmmt) cc_final: 0.7072 (ptmm) REVERT: C 144 GLU cc_start: 0.7091 (tp30) cc_final: 0.6816 (tp30) REVERT: C 159 ASP cc_start: 0.7638 (t0) cc_final: 0.7009 (t0) REVERT: C 164 MET cc_start: 0.8550 (ppp) cc_final: 0.8227 (ppp) REVERT: C 199 TYR cc_start: 0.7828 (t80) cc_final: 0.7618 (t80) REVERT: C 204 TYR cc_start: 0.7692 (m-80) cc_final: 0.7431 (m-10) REVERT: C 225 CYS cc_start: 0.8554 (m) cc_final: 0.8333 (m) REVERT: C 236 LYS cc_start: 0.8692 (mppt) cc_final: 0.8112 (mppt) REVERT: C 244 GLN cc_start: 0.6004 (tp-100) cc_final: 0.5713 (tp40) REVERT: C 263 ARG cc_start: 0.8304 (ptt180) cc_final: 0.6798 (ptt180) REVERT: C 267 ARG cc_start: 0.7981 (ppt170) cc_final: 0.7668 (ppt170) REVERT: C 292 GLU cc_start: 0.8491 (pm20) cc_final: 0.8155 (pm20) REVERT: C 302 ASN cc_start: 0.8309 (t0) cc_final: 0.7993 (m110) REVERT: C 306 MET cc_start: 0.7975 (tmm) cc_final: 0.7340 (tmm) REVERT: C 308 ARG cc_start: 0.8844 (ttp-170) cc_final: 0.8599 (ttm-80) REVERT: C 323 GLN cc_start: 0.8764 (mt0) cc_final: 0.8430 (mm110) REVERT: C 344 TYR cc_start: 0.8922 (m-10) cc_final: 0.8681 (m-10) REVERT: C 350 LEU cc_start: 0.8695 (mm) cc_final: 0.8494 (mm) REVERT: C 351 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8630 (tttm) REVERT: C 357 GLN cc_start: 0.7991 (tt0) cc_final: 0.7347 (tt0) REVERT: C 365 ASP cc_start: 0.7839 (p0) cc_final: 0.7591 (p0) REVERT: C 367 VAL cc_start: 0.8944 (t) cc_final: 0.8607 (p) REVERT: C 398 GLU cc_start: 0.8047 (tt0) cc_final: 0.7358 (tt0) REVERT: C 442 CYS cc_start: 0.6578 (p) cc_final: 0.6096 (m) REVERT: C 445 LYS cc_start: 0.8051 (mttp) cc_final: 0.7604 (mttm) REVERT: C 449 SER cc_start: 0.8634 (t) cc_final: 0.8426 (t) REVERT: C 464 GLU cc_start: 0.6856 (mp0) cc_final: 0.6654 (mp0) REVERT: C 476 PHE cc_start: 0.8007 (m-80) cc_final: 0.7745 (m-80) REVERT: C 504 GLU cc_start: 0.8463 (tp30) cc_final: 0.7969 (tp30) REVERT: C 550 LYS cc_start: 0.8352 (mttt) cc_final: 0.8133 (mttt) REVERT: C 557 LEU cc_start: 0.8875 (mm) cc_final: 0.8517 (mm) REVERT: C 566 LYS cc_start: 0.8676 (pttp) cc_final: 0.8272 (pttp) REVERT: C 584 HIS cc_start: 0.8483 (m90) cc_final: 0.8209 (m90) REVERT: C 590 LYS cc_start: 0.8259 (ttpp) cc_final: 0.7987 (ttpp) REVERT: C 606 LEU cc_start: 0.8716 (mp) cc_final: 0.8449 (mp) REVERT: D 32 ASN cc_start: 0.9094 (t0) cc_final: 0.8876 (t0) REVERT: D 78 ASN cc_start: 0.8992 (t0) cc_final: 0.8241 (t0) REVERT: D 103 HIS cc_start: 0.6847 (m-70) cc_final: 0.6591 (m-70) outliers start: 0 outliers final: 0 residues processed: 447 average time/residue: 0.1065 time to fit residues: 67.4156 Evaluate side-chains 414 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 146 optimal weight: 0.0870 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.0050 chunk 58 optimal weight: 0.4980 overall best weight: 0.4772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN C 415 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.157574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.123117 restraints weight = 29935.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127455 restraints weight = 17238.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.130419 restraints weight = 11341.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.132458 restraints weight = 8054.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.133965 restraints weight = 6175.390| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14205 Z= 0.140 Angle : 0.735 12.693 19562 Z= 0.383 Chirality : 0.044 0.192 2195 Planarity : 0.005 0.058 2244 Dihedral : 21.376 160.257 2554 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.08 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.21), residues: 1535 helix: -0.03 (0.21), residues: 591 sheet: -0.46 (0.36), residues: 224 loop : -1.73 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 472 TYR 0.034 0.002 TYR A 41 PHE 0.068 0.002 PHE A 589 TRP 0.028 0.002 TRP A 259 HIS 0.011 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (14204) covalent geometry : angle 0.73536 / 0.38 (19562) hydrogen bonds : bond 0.04516 / 2.99 ( 580) hydrogen bonds : angle 5.24113 / 3.71 ( 1605) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8607 (t70) cc_final: 0.8258 (t0) REVERT: A 66 PHE cc_start: 0.7230 (m-80) cc_final: 0.6893 (m-80) REVERT: A 119 ASP cc_start: 0.8784 (p0) cc_final: 0.8584 (p0) REVERT: A 181 ARG cc_start: 0.8641 (ttp80) cc_final: 0.7978 (ttp80) REVERT: A 222 LEU cc_start: 0.8820 (tp) cc_final: 0.8604 (tp) REVERT: A 231 LYS cc_start: 0.8965 (mptt) cc_final: 0.8693 (mptt) REVERT: A 255 LEU cc_start: 0.7731 (mt) cc_final: 0.7461 (mt) REVERT: A 260 ASP cc_start: 0.7709 (p0) cc_final: 0.7480 (p0) REVERT: A 272 MET cc_start: 0.7816 (mtt) cc_final: 0.7436 (mtt) REVERT: A 290 ARG cc_start: 0.8438 (ppt170) cc_final: 0.8049 (pmt-80) REVERT: A 293 LYS cc_start: 0.7941 (pttm) cc_final: 0.7282 (pttm) REVERT: A 297 ARG cc_start: 0.6094 (ptm160) cc_final: 0.5704 (ptm160) REVERT: A 305 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8188 (tp30) REVERT: A 316 MET cc_start: 0.6831 (tmm) cc_final: 0.6602 (tmm) REVERT: A 346 GLU cc_start: 0.7813 (mp0) cc_final: 0.7480 (mp0) REVERT: A 366 THR cc_start: 0.8507 (p) cc_final: 0.8269 (p) REVERT: A 368 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8463 (mtpt) REVERT: A 369 ARG cc_start: 0.9073 (ptm-80) cc_final: 0.8650 (ptm-80) REVERT: A 370 LEU cc_start: 0.8886 (tt) cc_final: 0.8441 (tt) REVERT: A 379 ARG cc_start: 0.7751 (mtp85) cc_final: 0.7473 (mtp85) REVERT: A 382 HIS cc_start: 0.7152 (t-90) cc_final: 0.6937 (t-90) REVERT: A 398 GLU cc_start: 0.7423 (pm20) cc_final: 0.7130 (pm20) REVERT: A 409 TYR cc_start: 0.8668 (t80) cc_final: 0.8308 (t80) REVERT: A 426 TYR cc_start: 0.7001 (p90) cc_final: 0.6593 (p90) REVERT: A 482 LYS cc_start: 0.7819 (mmmm) cc_final: 0.7182 (mmmm) REVERT: A 489 ASN cc_start: 0.7003 (p0) cc_final: 0.6780 (p0) REVERT: A 502 LEU cc_start: 0.9068 (pp) cc_final: 0.8584 (pp) REVERT: A 516 VAL cc_start: 0.8805 (m) cc_final: 0.8306 (p) REVERT: A 518 ILE cc_start: 0.8908 (mm) cc_final: 0.8674 (tp) REVERT: A 520 ASN cc_start: 0.8791 (m-40) cc_final: 0.8457 (m-40) REVERT: A 525 ASN cc_start: 0.6868 (m-40) cc_final: 0.6284 (m110) REVERT: A 560 ILE cc_start: 0.8152 (mt) cc_final: 0.7846 (pt) REVERT: A 565 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 569 ASN cc_start: 0.7122 (m110) cc_final: 0.6798 (m110) REVERT: A 603 MET cc_start: 0.8484 (mtm) cc_final: 0.8227 (mtm) REVERT: B 99 MET cc_start: 0.5876 (tpt) cc_final: 0.5464 (tpt) REVERT: B 136 LYS cc_start: 0.7858 (mmpt) cc_final: 0.7142 (mmpt) REVERT: C 32 LEU cc_start: 0.7931 (mt) cc_final: 0.7688 (mt) REVERT: C 53 LYS cc_start: 0.6949 (mppt) cc_final: 0.6395 (mppt) REVERT: C 71 ASN cc_start: 0.7813 (m-40) cc_final: 0.7504 (m110) REVERT: C 90 LYS cc_start: 0.8439 (ptmm) cc_final: 0.8225 (ptmm) REVERT: C 95 LYS cc_start: 0.9057 (mppt) cc_final: 0.8601 (mppt) REVERT: C 98 MET cc_start: 0.7423 (ttt) cc_final: 0.6882 (ttt) REVERT: C 128 GLU cc_start: 0.7344 (mt-10) cc_final: 0.6802 (mt-10) REVERT: C 144 GLU cc_start: 0.7102 (tp30) cc_final: 0.6831 (tp30) REVERT: C 159 ASP cc_start: 0.7584 (t0) cc_final: 0.6922 (t0) REVERT: C 164 MET cc_start: 0.8552 (ppp) cc_final: 0.8202 (ppp) REVERT: C 199 TYR cc_start: 0.7841 (t80) cc_final: 0.7595 (t80) REVERT: C 204 TYR cc_start: 0.7684 (m-80) cc_final: 0.7374 (m-10) REVERT: C 218 GLN cc_start: 0.7550 (mt0) cc_final: 0.7139 (mt0) REVERT: C 236 LYS cc_start: 0.8699 (mppt) cc_final: 0.8123 (mppt) REVERT: C 244 GLN cc_start: 0.5999 (tp-100) cc_final: 0.5715 (tp40) REVERT: C 263 ARG cc_start: 0.8288 (ptt180) cc_final: 0.6818 (ptt180) REVERT: C 267 ARG cc_start: 0.8016 (ppt170) cc_final: 0.7681 (ppt170) REVERT: C 292 GLU cc_start: 0.8482 (pm20) cc_final: 0.8189 (pm20) REVERT: C 302 ASN cc_start: 0.8320 (t0) cc_final: 0.8038 (m110) REVERT: C 305 GLU cc_start: 0.8116 (tp30) cc_final: 0.7881 (tp30) REVERT: C 306 MET cc_start: 0.7986 (tmm) cc_final: 0.7407 (tmm) REVERT: C 307 LEU cc_start: 0.8837 (mt) cc_final: 0.8560 (mt) REVERT: C 308 ARG cc_start: 0.8785 (ttp-170) cc_final: 0.7542 (ttm-80) REVERT: C 316 MET cc_start: 0.7163 (mtt) cc_final: 0.6874 (mtt) REVERT: C 323 GLN cc_start: 0.8754 (mt0) cc_final: 0.8429 (mm110) REVERT: C 351 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8622 (tttm) REVERT: C 357 GLN cc_start: 0.7971 (tt0) cc_final: 0.7332 (tt0) REVERT: C 365 ASP cc_start: 0.7840 (p0) cc_final: 0.7549 (p0) REVERT: C 367 VAL cc_start: 0.8941 (t) cc_final: 0.8600 (p) REVERT: C 382 HIS cc_start: 0.7988 (t70) cc_final: 0.7732 (t-90) REVERT: C 398 GLU cc_start: 0.7938 (tt0) cc_final: 0.7334 (tt0) REVERT: C 442 CYS cc_start: 0.6504 (p) cc_final: 0.6038 (m) REVERT: C 445 LYS cc_start: 0.8079 (mttp) cc_final: 0.7577 (mmtp) REVERT: C 449 SER cc_start: 0.8614 (t) cc_final: 0.8406 (t) REVERT: C 464 GLU cc_start: 0.6902 (mp0) cc_final: 0.6653 (mp0) REVERT: C 465 GLU cc_start: 0.6993 (tp30) cc_final: 0.6698 (tp30) REVERT: C 476 PHE cc_start: 0.7987 (m-80) cc_final: 0.7715 (m-80) REVERT: C 494 LEU cc_start: 0.8039 (tp) cc_final: 0.7721 (tt) REVERT: C 504 GLU cc_start: 0.8394 (tp30) cc_final: 0.7968 (tp30) REVERT: C 550 LYS cc_start: 0.8348 (mttt) cc_final: 0.8109 (mttt) REVERT: C 557 LEU cc_start: 0.8907 (mm) cc_final: 0.8620 (mm) REVERT: C 566 LYS cc_start: 0.8663 (pttp) cc_final: 0.8255 (pttp) REVERT: C 584 HIS cc_start: 0.8493 (m90) cc_final: 0.8234 (m90) REVERT: C 590 LYS cc_start: 0.8219 (ttpp) cc_final: 0.7983 (ttpp) REVERT: C 603 MET cc_start: 0.7501 (mtt) cc_final: 0.7265 (mtt) REVERT: C 606 LEU cc_start: 0.8714 (mp) cc_final: 0.8451 (mp) REVERT: D 18 ASP cc_start: 0.6030 (m-30) cc_final: 0.5540 (m-30) REVERT: D 32 ASN cc_start: 0.9077 (t0) cc_final: 0.8861 (t0) REVERT: D 78 ASN cc_start: 0.8963 (t0) cc_final: 0.8260 (t0) REVERT: D 103 HIS cc_start: 0.6827 (m-70) cc_final: 0.6585 (m-70) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.1128 time to fit residues: 71.3646 Evaluate side-chains 416 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 122 optimal weight: 0.0870 chunk 130 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.156853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122364 restraints weight = 29964.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126757 restraints weight = 17203.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129735 restraints weight = 11290.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.131844 restraints weight = 8000.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.133323 restraints weight = 6103.442| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14205 Z= 0.148 Angle : 0.741 12.058 19562 Z= 0.384 Chirality : 0.044 0.197 2195 Planarity : 0.005 0.056 2244 Dihedral : 21.371 160.374 2554 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.21), residues: 1535 helix: -0.01 (0.21), residues: 591 sheet: -0.55 (0.34), residues: 243 loop : -1.68 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 472 TYR 0.022 0.002 TYR C 549 PHE 0.023 0.001 PHE A 589 TRP 0.024 0.002 TRP A 259 HIS 0.011 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (14204) covalent geometry : angle 0.74107 / 0.38 (19562) hydrogen bonds : bond 0.04502 / 2.99 ( 580) hydrogen bonds : angle 5.21271 / 3.72 ( 1605) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 445 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ARG cc_start: 0.8222 (pmt170) cc_final: 0.7582 (ptp90) REVERT: A 62 MET cc_start: 0.6091 (tmm) cc_final: 0.5873 (tmm) REVERT: A 65 ASP cc_start: 0.8595 (t70) cc_final: 0.8231 (t0) REVERT: A 66 PHE cc_start: 0.7193 (m-80) cc_final: 0.6814 (m-80) REVERT: A 119 ASP cc_start: 0.8828 (p0) cc_final: 0.8615 (p0) REVERT: A 164 MET cc_start: 0.9158 (ptp) cc_final: 0.8843 (ptp) REVERT: A 181 ARG cc_start: 0.8669 (ttp80) cc_final: 0.8171 (ttp80) REVERT: A 222 LEU cc_start: 0.8847 (tp) cc_final: 0.8632 (tp) REVERT: A 231 LYS cc_start: 0.8978 (mptt) cc_final: 0.8706 (mptt) REVERT: A 236 LYS cc_start: 0.8825 (mmmt) cc_final: 0.8538 (tppt) REVERT: A 246 LYS cc_start: 0.7841 (pptt) cc_final: 0.7079 (tmtt) REVERT: A 255 LEU cc_start: 0.7755 (mt) cc_final: 0.7474 (mt) REVERT: A 260 ASP cc_start: 0.7796 (p0) cc_final: 0.7548 (p0) REVERT: A 272 MET cc_start: 0.7877 (mtt) cc_final: 0.7547 (mtt) REVERT: A 290 ARG cc_start: 0.8444 (ppt170) cc_final: 0.8041 (pmt-80) REVERT: A 293 LYS cc_start: 0.7938 (pttm) cc_final: 0.7585 (pttm) REVERT: A 297 ARG cc_start: 0.6096 (ptm160) cc_final: 0.5725 (ptm160) REVERT: A 305 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8199 (tp30) REVERT: A 316 MET cc_start: 0.6772 (tmm) cc_final: 0.6354 (tmm) REVERT: A 320 HIS cc_start: 0.7251 (t-90) cc_final: 0.7008 (t-90) REVERT: A 346 GLU cc_start: 0.7819 (mp0) cc_final: 0.7479 (mp0) REVERT: A 348 PHE cc_start: 0.8764 (t80) cc_final: 0.8512 (t80) REVERT: A 355 ARG cc_start: 0.8334 (ttm110) cc_final: 0.8004 (ttm110) REVERT: A 366 THR cc_start: 0.8445 (p) cc_final: 0.8219 (p) REVERT: A 368 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8466 (mtpt) REVERT: A 369 ARG cc_start: 0.9089 (ptm-80) cc_final: 0.8665 (ptm-80) REVERT: A 370 LEU cc_start: 0.8911 (tt) cc_final: 0.8477 (tt) REVERT: A 379 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7465 (mtp85) REVERT: A 382 HIS cc_start: 0.7266 (t-90) cc_final: 0.6971 (t-90) REVERT: A 398 GLU cc_start: 0.7422 (pm20) cc_final: 0.7090 (pm20) REVERT: A 406 TRP cc_start: 0.8885 (t60) cc_final: 0.8247 (t60) REVERT: A 409 TYR cc_start: 0.8673 (t80) cc_final: 0.8279 (t80) REVERT: A 410 GLU cc_start: 0.8516 (tt0) cc_final: 0.8231 (tt0) REVERT: A 482 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7201 (mmmm) REVERT: A 489 ASN cc_start: 0.6937 (p0) cc_final: 0.6732 (p0) REVERT: A 502 LEU cc_start: 0.9069 (pp) cc_final: 0.8611 (pp) REVERT: A 516 VAL cc_start: 0.8824 (m) cc_final: 0.8294 (p) REVERT: A 519 ASN cc_start: 0.7820 (m110) cc_final: 0.7504 (m110) REVERT: A 520 ASN cc_start: 0.8789 (m-40) cc_final: 0.8477 (m-40) REVERT: A 525 ASN cc_start: 0.6819 (m-40) cc_final: 0.6243 (m110) REVERT: A 560 ILE cc_start: 0.8179 (mt) cc_final: 0.7853 (pt) REVERT: A 565 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7612 (mt-10) REVERT: A 569 ASN cc_start: 0.7174 (m110) cc_final: 0.6846 (m110) REVERT: A 585 THR cc_start: 0.7868 (t) cc_final: 0.7540 (t) REVERT: A 603 MET cc_start: 0.8473 (mtm) cc_final: 0.8225 (mtm) REVERT: B 71 LEU cc_start: 0.8029 (mt) cc_final: 0.7236 (mt) REVERT: B 99 MET cc_start: 0.5901 (tpt) cc_final: 0.5522 (tpt) REVERT: B 128 LYS cc_start: 0.8420 (tttm) cc_final: 0.8142 (tttm) REVERT: B 136 LYS cc_start: 0.7811 (mmpt) cc_final: 0.7094 (mmpt) REVERT: C 32 LEU cc_start: 0.7931 (mt) cc_final: 0.7664 (mt) REVERT: C 53 LYS cc_start: 0.6923 (mppt) cc_final: 0.6393 (mppt) REVERT: C 71 ASN cc_start: 0.7741 (m-40) cc_final: 0.7418 (m110) REVERT: C 90 LYS cc_start: 0.8456 (ptmm) cc_final: 0.8155 (ptmm) REVERT: C 95 LYS cc_start: 0.9052 (mppt) cc_final: 0.8603 (mppt) REVERT: C 98 MET cc_start: 0.7488 (ttt) cc_final: 0.6911 (ttt) REVERT: C 128 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6920 (mt-10) REVERT: C 144 GLU cc_start: 0.7075 (tp30) cc_final: 0.6811 (tp30) REVERT: C 159 ASP cc_start: 0.7589 (t0) cc_final: 0.6910 (t0) REVERT: C 164 MET cc_start: 0.8516 (ppp) cc_final: 0.8149 (ppp) REVERT: C 199 TYR cc_start: 0.7842 (t80) cc_final: 0.7571 (t80) REVERT: C 203 LYS cc_start: 0.7171 (ptpp) cc_final: 0.6927 (pttm) REVERT: C 204 TYR cc_start: 0.7710 (m-80) cc_final: 0.7337 (m-10) REVERT: C 218 GLN cc_start: 0.7537 (mt0) cc_final: 0.7118 (mt0) REVERT: C 236 LYS cc_start: 0.8711 (mppt) cc_final: 0.8137 (mppt) REVERT: C 244 GLN cc_start: 0.5986 (tp-100) cc_final: 0.5721 (tp40) REVERT: C 263 ARG cc_start: 0.8286 (ptt180) cc_final: 0.6936 (ptt180) REVERT: C 267 ARG cc_start: 0.8030 (ppt170) cc_final: 0.7695 (ppt170) REVERT: C 292 GLU cc_start: 0.8459 (pm20) cc_final: 0.8199 (pm20) REVERT: C 301 LEU cc_start: 0.8459 (tp) cc_final: 0.8154 (tp) REVERT: C 302 ASN cc_start: 0.8256 (t0) cc_final: 0.8040 (m110) REVERT: C 305 GLU cc_start: 0.8099 (tp30) cc_final: 0.7889 (tp30) REVERT: C 306 MET cc_start: 0.8014 (tmm) cc_final: 0.7455 (tmm) REVERT: C 307 LEU cc_start: 0.8839 (mt) cc_final: 0.8569 (mt) REVERT: C 308 ARG cc_start: 0.8771 (ttp-170) cc_final: 0.8307 (tpp80) REVERT: C 316 MET cc_start: 0.7254 (mtt) cc_final: 0.6964 (mtt) REVERT: C 323 GLN cc_start: 0.8769 (mt0) cc_final: 0.8457 (mm110) REVERT: C 350 LEU cc_start: 0.8729 (mm) cc_final: 0.8515 (mm) REVERT: C 351 LYS cc_start: 0.8932 (ttmm) cc_final: 0.8614 (tttm) REVERT: C 357 GLN cc_start: 0.7988 (tt0) cc_final: 0.7280 (tt0) REVERT: C 365 ASP cc_start: 0.7854 (p0) cc_final: 0.7564 (p0) REVERT: C 367 VAL cc_start: 0.8970 (t) cc_final: 0.8619 (p) REVERT: C 382 HIS cc_start: 0.8002 (t70) cc_final: 0.7754 (t-90) REVERT: C 442 CYS cc_start: 0.6641 (p) cc_final: 0.6176 (m) REVERT: C 445 LYS cc_start: 0.8014 (mttp) cc_final: 0.7730 (mmtp) REVERT: C 449 SER cc_start: 0.8626 (t) cc_final: 0.8425 (t) REVERT: C 465 GLU cc_start: 0.6959 (tp30) cc_final: 0.6657 (tp30) REVERT: C 474 ASP cc_start: 0.8281 (p0) cc_final: 0.8015 (p0) REVERT: C 476 PHE cc_start: 0.8019 (m-80) cc_final: 0.7760 (m-80) REVERT: C 494 LEU cc_start: 0.8090 (tp) cc_final: 0.7823 (tt) REVERT: C 504 GLU cc_start: 0.8420 (tp30) cc_final: 0.7971 (tp30) REVERT: C 550 LYS cc_start: 0.8357 (mttt) cc_final: 0.8127 (mttt) REVERT: C 557 LEU cc_start: 0.8935 (mm) cc_final: 0.8644 (mm) REVERT: C 566 LYS cc_start: 0.8710 (pttp) cc_final: 0.8296 (pttp) REVERT: C 584 HIS cc_start: 0.8526 (m90) cc_final: 0.8230 (m90) REVERT: C 603 MET cc_start: 0.7512 (mtt) cc_final: 0.7245 (mtt) REVERT: C 606 LEU cc_start: 0.8723 (mp) cc_final: 0.8477 (mp) REVERT: D 32 ASN cc_start: 0.9105 (t0) cc_final: 0.8884 (t0) REVERT: D 78 ASN cc_start: 0.9040 (t0) cc_final: 0.8639 (t0) REVERT: D 103 HIS cc_start: 0.6850 (m-70) cc_final: 0.6601 (m-70) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.1239 time to fit residues: 78.1934 Evaluate side-chains 422 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 52 optimal weight: 0.0020 chunk 73 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 overall best weight: 0.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.158222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.123515 restraints weight = 29832.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.127907 restraints weight = 17254.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.130934 restraints weight = 11275.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133011 restraints weight = 8036.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134494 restraints weight = 6168.900| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14205 Z= 0.146 Angle : 0.770 12.065 19562 Z= 0.399 Chirality : 0.045 0.192 2195 Planarity : 0.005 0.058 2244 Dihedral : 21.362 160.169 2554 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.21), residues: 1535 helix: -0.05 (0.21), residues: 591 sheet: -0.45 (0.36), residues: 224 loop : -1.68 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 46 TYR 0.032 0.002 TYR A 41 PHE 0.039 0.001 PHE A 589 TRP 0.049 0.003 TRP D 14 HIS 0.011 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 (14204) covalent geometry : angle 0.76961 / 0.40 (19562) hydrogen bonds : bond 0.04468 / 2.96 ( 580) hydrogen bonds : angle 5.23967 / 3.73 ( 1605) Misc. bond : bond 0.00094 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 MET cc_start: 0.6286 (tmm) cc_final: 0.6050 (tmm) REVERT: A 51 ARG cc_start: 0.8269 (pmt170) cc_final: 0.7692 (ptp90) REVERT: A 55 THR cc_start: 0.6798 (p) cc_final: 0.6512 (t) REVERT: A 65 ASP cc_start: 0.8589 (t70) cc_final: 0.8210 (t0) REVERT: A 66 PHE cc_start: 0.7176 (m-80) cc_final: 0.6805 (m-80) REVERT: A 119 ASP cc_start: 0.8831 (p0) cc_final: 0.8615 (p0) REVERT: A 164 MET cc_start: 0.9153 (ptp) cc_final: 0.8837 (ptp) REVERT: A 181 ARG cc_start: 0.8713 (ttp80) cc_final: 0.8212 (ttp80) REVERT: A 222 LEU cc_start: 0.8853 (tp) cc_final: 0.8634 (tp) REVERT: A 224 PHE cc_start: 0.8140 (m-10) cc_final: 0.7885 (m-10) REVERT: A 231 LYS cc_start: 0.8964 (mptt) cc_final: 0.8687 (mptt) REVERT: A 255 LEU cc_start: 0.7766 (mt) cc_final: 0.7470 (mt) REVERT: A 260 ASP cc_start: 0.7795 (p0) cc_final: 0.7560 (p0) REVERT: A 272 MET cc_start: 0.7833 (mtt) cc_final: 0.7480 (mtt) REVERT: A 290 ARG cc_start: 0.8430 (ppt170) cc_final: 0.8022 (pmt-80) REVERT: A 293 LYS cc_start: 0.7938 (pttm) cc_final: 0.7592 (pttm) REVERT: A 297 ARG cc_start: 0.6142 (ptm160) cc_final: 0.5770 (ptm160) REVERT: A 305 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8186 (tp30) REVERT: A 316 MET cc_start: 0.6679 (tmm) cc_final: 0.6233 (tmm) REVERT: A 320 HIS cc_start: 0.7237 (t-90) cc_final: 0.6979 (t-90) REVERT: A 346 GLU cc_start: 0.7815 (mp0) cc_final: 0.7496 (mp0) REVERT: A 348 PHE cc_start: 0.8750 (t80) cc_final: 0.8197 (t80) REVERT: A 351 LYS cc_start: 0.8437 (tppt) cc_final: 0.7738 (mmtm) REVERT: A 355 ARG cc_start: 0.8262 (ttm110) cc_final: 0.7808 (ttm110) REVERT: A 366 THR cc_start: 0.8409 (p) cc_final: 0.8193 (p) REVERT: A 368 LYS cc_start: 0.8799 (mtpt) cc_final: 0.8453 (mtpt) REVERT: A 369 ARG cc_start: 0.9082 (ptm-80) cc_final: 0.8656 (ptm-80) REVERT: A 370 LEU cc_start: 0.8903 (tt) cc_final: 0.8467 (tt) REVERT: A 379 ARG cc_start: 0.7745 (mtp85) cc_final: 0.7511 (mtp85) REVERT: A 382 HIS cc_start: 0.7279 (t-90) cc_final: 0.6988 (t-90) REVERT: A 409 TYR cc_start: 0.8656 (t80) cc_final: 0.8279 (t80) REVERT: A 489 ASN cc_start: 0.6880 (p0) cc_final: 0.6679 (p0) REVERT: A 502 LEU cc_start: 0.9047 (pp) cc_final: 0.8616 (pp) REVERT: A 516 VAL cc_start: 0.8790 (m) cc_final: 0.8328 (p) REVERT: A 520 ASN cc_start: 0.8757 (m-40) cc_final: 0.8434 (m-40) REVERT: A 525 ASN cc_start: 0.6765 (m-40) cc_final: 0.6202 (m110) REVERT: A 560 ILE cc_start: 0.8120 (mt) cc_final: 0.7813 (pt) REVERT: A 565 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 569 ASN cc_start: 0.7133 (m110) cc_final: 0.6772 (m110) REVERT: A 585 THR cc_start: 0.7836 (t) cc_final: 0.7561 (t) REVERT: A 603 MET cc_start: 0.8454 (mtm) cc_final: 0.8160 (mtm) REVERT: B 71 LEU cc_start: 0.7998 (mt) cc_final: 0.7184 (mt) REVERT: B 99 MET cc_start: 0.5888 (tpt) cc_final: 0.5498 (tpt) REVERT: B 128 LYS cc_start: 0.8419 (tttm) cc_final: 0.8133 (tttm) REVERT: B 136 LYS cc_start: 0.7871 (mmpt) cc_final: 0.7181 (mmpt) REVERT: C 32 LEU cc_start: 0.7910 (mt) cc_final: 0.7659 (mt) REVERT: C 53 LYS cc_start: 0.6896 (mppt) cc_final: 0.6379 (mppt) REVERT: C 71 ASN cc_start: 0.7732 (m-40) cc_final: 0.7461 (m110) REVERT: C 95 LYS cc_start: 0.9036 (mppt) cc_final: 0.8581 (mppt) REVERT: C 98 MET cc_start: 0.7469 (ttt) cc_final: 0.6914 (ttt) REVERT: C 128 GLU cc_start: 0.7399 (mt-10) cc_final: 0.6858 (mt-10) REVERT: C 144 GLU cc_start: 0.7063 (tp30) cc_final: 0.6800 (tp30) REVERT: C 159 ASP cc_start: 0.7536 (t0) cc_final: 0.6775 (t0) REVERT: C 164 MET cc_start: 0.8496 (ppp) cc_final: 0.8138 (ppp) REVERT: C 203 LYS cc_start: 0.7182 (ptpp) cc_final: 0.6956 (pttm) REVERT: C 204 TYR cc_start: 0.7716 (m-80) cc_final: 0.7357 (m-10) REVERT: C 218 GLN cc_start: 0.7537 (mt0) cc_final: 0.7120 (mt0) REVERT: C 236 LYS cc_start: 0.8712 (mppt) cc_final: 0.8134 (mppt) REVERT: C 244 GLN cc_start: 0.5949 (tp-100) cc_final: 0.5681 (tp-100) REVERT: C 263 ARG cc_start: 0.8259 (ptt180) cc_final: 0.6914 (ptt180) REVERT: C 267 ARG cc_start: 0.8006 (ppt170) cc_final: 0.7642 (ppt170) REVERT: C 292 GLU cc_start: 0.8446 (pm20) cc_final: 0.8179 (pm20) REVERT: C 301 LEU cc_start: 0.8460 (tp) cc_final: 0.8157 (tp) REVERT: C 306 MET cc_start: 0.8007 (tmm) cc_final: 0.7445 (tmm) REVERT: C 307 LEU cc_start: 0.8855 (mt) cc_final: 0.8592 (mt) REVERT: C 308 ARG cc_start: 0.8729 (ttp-170) cc_final: 0.8277 (tpp80) REVERT: C 316 MET cc_start: 0.7242 (mtt) cc_final: 0.6969 (mtt) REVERT: C 351 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8603 (tttm) REVERT: C 357 GLN cc_start: 0.7932 (tt0) cc_final: 0.7326 (tt0) REVERT: C 365 ASP cc_start: 0.7820 (p0) cc_final: 0.7545 (p0) REVERT: C 367 VAL cc_start: 0.8951 (t) cc_final: 0.8639 (p) REVERT: C 442 CYS cc_start: 0.6564 (p) cc_final: 0.6116 (m) REVERT: C 445 LYS cc_start: 0.8029 (mttp) cc_final: 0.7586 (mmtp) REVERT: C 464 GLU cc_start: 0.6887 (mp0) cc_final: 0.6626 (mp0) REVERT: C 465 GLU cc_start: 0.6969 (tp30) cc_final: 0.6654 (tp30) REVERT: C 476 PHE cc_start: 0.8004 (m-80) cc_final: 0.7700 (m-80) REVERT: C 494 LEU cc_start: 0.8099 (tp) cc_final: 0.7821 (tt) REVERT: C 504 GLU cc_start: 0.8374 (tp30) cc_final: 0.7971 (tp30) REVERT: C 550 LYS cc_start: 0.8348 (mttt) cc_final: 0.8117 (mttt) REVERT: C 557 LEU cc_start: 0.8920 (mm) cc_final: 0.8627 (mm) REVERT: C 566 LYS cc_start: 0.8695 (pttp) cc_final: 0.8265 (pttp) REVERT: C 584 HIS cc_start: 0.8523 (m90) cc_final: 0.8258 (m90) REVERT: C 603 MET cc_start: 0.7502 (mtt) cc_final: 0.7258 (mtt) REVERT: C 606 LEU cc_start: 0.8734 (mp) cc_final: 0.8490 (mp) REVERT: D 32 ASN cc_start: 0.9013 (t0) cc_final: 0.8808 (t0) REVERT: D 78 ASN cc_start: 0.8981 (t0) cc_final: 0.8257 (t0) REVERT: D 99 MET cc_start: 0.7422 (ttt) cc_final: 0.6763 (ttt) REVERT: D 103 HIS cc_start: 0.6835 (m-70) cc_final: 0.6597 (m-70) REVERT: D 157 LEU cc_start: 0.8493 (mm) cc_final: 0.8205 (mm) REVERT: D 159 GLU cc_start: 0.8296 (mp0) cc_final: 0.8060 (mp0) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.1230 time to fit residues: 77.8663 Evaluate side-chains 420 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 123 optimal weight: 0.0370 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 0.0020 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.5666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.157569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.122345 restraints weight = 30604.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.126748 restraints weight = 17712.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.129799 restraints weight = 11678.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131920 restraints weight = 8309.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133410 restraints weight = 6388.339| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 14205 Z= 0.147 Angle : 0.746 11.905 19562 Z= 0.388 Chirality : 0.045 0.193 2195 Planarity : 0.005 0.057 2244 Dihedral : 21.350 160.376 2554 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.14 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.21), residues: 1535 helix: -0.06 (0.21), residues: 590 sheet: -0.46 (0.34), residues: 242 loop : -1.68 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 46 TYR 0.021 0.002 TYR A 595 PHE 0.035 0.002 PHE A 589 TRP 0.027 0.002 TRP C 458 HIS 0.010 0.001 HIS A 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (14204) covalent geometry : angle 0.74615 / 0.39 (19562) hydrogen bonds : bond 0.04458 / 2.96 ( 580) hydrogen bonds : angle 5.17366 / 3.67 ( 1605) Misc. bond : bond 0.00090 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2409.36 seconds wall clock time: 42 minutes 22.77 seconds (2542.77 seconds total)