Starting phenix.real_space_refine on Fri May 16 00:13:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9w_45374/05_2025/9c9w_45374_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9w_45374/05_2025/9c9w_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_45374/05_2025/9c9w_45374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9w_45374/05_2025/9c9w_45374.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9w_45374/05_2025/9c9w_45374_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9w_45374/05_2025/9c9w_45374_neut.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.35, per 1000 atoms: 0.61 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: 3.70 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 5.21 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: 5.66 Time building geometry restraints manager: 4.20 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=" 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=" N HIS A 387 " pdb=" CA HIS A 387 " ideal model delta sigma weight residual 1.456 1.485 -0.029 9.80e-03 1.04e+04 8.61e+00 bond pdb=" C LEU A 328 " pdb=" O LEU A 328 " ideal model delta sigma weight residual 1.237 1.266 -0.030 1.16e-02 7.43e+03 6.62e+00 bond pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.27e-02 6.20e+03 5.24e+00 ... (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=" CA GLN A 331 " pdb=" C GLN A 331 " pdb=" N GLY A 332 " ideal model delta sigma weight residual 118.43 110.86 7.57 1.33e+00 5.65e-01 3.24e+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: 1686 0.045 - 0.091: 376 0.091 - 0.136: 115 0.136 - 0.182: 15 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: 3.470 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: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.610 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 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 : 0.005 0.476 14205 Z= 0.444 Angle : 0.802 28.764 19562 Z= 0.449 Chirality : 0.044 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 : 19.12 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (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 TRP 0.023 0.002 TRP C 363 HIS 0.005 0.001 HIS C 39 PHE 0.041 0.002 PHE A 589 TYR 0.026 0.002 TYR A 595 ARG 0.010 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.16309 ( 580) hydrogen bonds : angle 6.96821 ( 1605) covalent geometry : bond 0.00356 (14204) covalent geometry : angle 0.80187 (19562) Misc. bond : bond 0.47641 ( 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 : 1.348 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: 0.2966 time to fit residues: 189.0679 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 : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 0.0170 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 519 ASN A 523 GLN B 146 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124648 restraints weight = 29881.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129064 restraints weight = 17180.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.131983 restraints weight = 11172.351| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14205 Z= 0.149 Angle : 0.682 9.665 19562 Z= 0.361 Chirality : 0.042 0.206 2195 Planarity : 0.005 0.053 2244 Dihedral : 21.057 168.813 2554 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.79 % Favored : 91.14 % Rotamer: Outliers : 0.45 % Allowed : 5.39 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1535 helix: -0.09 (0.21), residues: 589 sheet: -0.48 (0.36), residues: 230 loop : -1.72 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 406 HIS 0.008 0.001 HIS C 60 PHE 0.027 0.001 PHE A 589 TYR 0.024 0.002 TYR A 595 ARG 0.007 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 580) hydrogen bonds : angle 5.51819 ( 1605) covalent geometry : bond 0.00316 (14204) covalent geometry : angle 0.68232 (19562) Misc. bond : bond 0.00069 ( 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 457 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 451 time to evaluate : 1.358 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 2 LYS cc_start: 0.9090 (mttt) cc_final: 0.8853 (mttp) REVERT: A 66 PHE cc_start: 0.7302 (m-80) cc_final: 0.7030 (m-80) REVERT: A 218 GLN cc_start: 0.8574 (mm110) cc_final: 0.8201 (mm110) REVERT: A 226 VAL cc_start: 0.8696 (p) cc_final: 0.8486 (p) REVERT: A 231 LYS cc_start: 0.8927 (mptt) cc_final: 0.8632 (mptt) REVERT: A 232 ILE cc_start: 0.8974 (mt) cc_final: 0.8764 (mt) REVERT: A 233 GLN cc_start: 0.8744 (mm110) cc_final: 0.8289 (mp10) REVERT: A 244 GLN cc_start: 0.8508 (tp40) cc_final: 0.8131 (tp-100) REVERT: A 255 LEU cc_start: 0.7753 (mt) cc_final: 0.7362 (mm) REVERT: A 260 ASP cc_start: 0.7627 (p0) cc_final: 0.7365 (p0) REVERT: A 271 GLN cc_start: 0.8466 (tp-100) cc_final: 0.8093 (tp-100) REVERT: A 272 MET cc_start: 0.7232 (mtt) cc_final: 0.6522 (mtt) REVERT: A 293 LYS cc_start: 0.7920 (pttm) cc_final: 0.7293 (pttm) REVERT: A 303 THR cc_start: 0.8167 (m) cc_final: 0.7871 (p) REVERT: A 305 GLU cc_start: 0.8614 (tt0) cc_final: 0.7854 (tp30) REVERT: A 323 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8107 (tm-30) REVERT: A 327 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8197 (tpp80) REVERT: A 346 GLU cc_start: 0.7625 (mp0) cc_final: 0.7321 (mp0) REVERT: A 351 LYS cc_start: 0.8594 (tttp) cc_final: 0.8252 (tppt) REVERT: A 355 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7811 (tpm170) REVERT: A 360 HIS cc_start: 0.8071 (t-90) cc_final: 0.7702 (t-90) REVERT: A 368 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8461 (mtpt) REVERT: A 370 LEU cc_start: 0.8850 (tt) cc_final: 0.8640 (tt) REVERT: A 376 ASN cc_start: 0.7549 (p0) cc_final: 0.7343 (p0) REVERT: A 380 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7987 (ttmt) REVERT: A 406 TRP cc_start: 0.8827 (t60) cc_final: 0.8505 (t60) REVERT: A 408 LEU cc_start: 0.8703 (tp) cc_final: 0.8202 (tp) REVERT: A 409 TYR cc_start: 0.8570 (t80) cc_final: 0.8281 (t80) REVERT: A 426 TYR cc_start: 0.6970 (p90) cc_final: 0.6603 (p90) REVERT: A 476 PHE cc_start: 0.7630 (m-80) cc_final: 0.7411 (m-80) REVERT: A 489 ASN cc_start: 0.7064 (p0) cc_final: 0.6742 (p0) REVERT: A 516 VAL cc_start: 0.8850 (m) cc_final: 0.8191 (p) REVERT: A 520 ASN cc_start: 0.8569 (m-40) cc_final: 0.8175 (m-40) REVERT: A 525 ASN cc_start: 0.6813 (m-40) cc_final: 0.6191 (m110) REVERT: A 565 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 603 MET cc_start: 0.8516 (mtm) cc_final: 0.8297 (mtm) REVERT: C 1 MET cc_start: 0.5587 (pmm) cc_final: 0.5302 (pmm) REVERT: C 6 MET cc_start: 0.7405 (ptm) cc_final: 0.7167 (ptm) REVERT: C 48 GLN cc_start: 0.7333 (mp10) cc_final: 0.7088 (mp10) REVERT: C 51 ARG cc_start: 0.6542 (ttp-110) cc_final: 0.6332 (ttp-110) REVERT: C 53 LYS cc_start: 0.7678 (mppt) cc_final: 0.6842 (mppt) REVERT: C 66 PHE cc_start: 0.7113 (m-80) cc_final: 0.6876 (m-80) REVERT: C 95 LYS cc_start: 0.9053 (mppt) cc_final: 0.8483 (mppt) REVERT: C 128 GLU cc_start: 0.7600 (mt-10) cc_final: 0.6998 (mt-10) REVERT: C 139 LYS cc_start: 0.7278 (tmmt) cc_final: 0.6951 (tttm) REVERT: C 199 TYR cc_start: 0.8021 (t80) cc_final: 0.7701 (t80) REVERT: C 204 TYR cc_start: 0.7561 (m-80) cc_final: 0.7258 (m-10) REVERT: C 232 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7445 (mp) REVERT: C 236 LYS cc_start: 0.8643 (mppt) cc_final: 0.8032 (mppt) REVERT: C 244 GLN cc_start: 0.5950 (tp-100) cc_final: 0.5736 (tp-100) REVERT: C 262 VAL cc_start: 0.8869 (m) cc_final: 0.8656 (p) REVERT: C 301 LEU cc_start: 0.8404 (tp) cc_final: 0.8164 (tp) REVERT: C 302 ASN cc_start: 0.8355 (t0) cc_final: 0.8031 (m-40) REVERT: C 306 MET cc_start: 0.7923 (tmm) cc_final: 0.7414 (tmm) REVERT: C 308 ARG cc_start: 0.8712 (ttp-170) cc_final: 0.7919 (ttm-80) REVERT: C 351 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8093 (mtpp) REVERT: C 356 GLN cc_start: 0.8774 (mt0) cc_final: 0.8467 (mt0) REVERT: C 357 GLN cc_start: 0.7907 (tt0) cc_final: 0.7270 (tt0) REVERT: C 365 ASP cc_start: 0.8164 (p0) cc_final: 0.7820 (p0) REVERT: C 368 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8703 (ttmm) REVERT: C 398 GLU cc_start: 0.7763 (tt0) cc_final: 0.6868 (tt0) REVERT: C 415 HIS cc_start: 0.8070 (t-90) cc_final: 0.7770 (t-90) REVERT: C 438 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7493 (tp30) REVERT: C 442 CYS cc_start: 0.6441 (p) cc_final: 0.5875 (m) REVERT: C 476 PHE cc_start: 0.7927 (m-80) cc_final: 0.7638 (m-80) REVERT: C 500 ILE cc_start: 0.9085 (mm) cc_final: 0.8440 (mm) REVERT: C 503 MET cc_start: 0.8319 (tpp) cc_final: 0.8022 (tpp) REVERT: C 504 GLU cc_start: 0.8592 (tp30) cc_final: 0.8124 (tp30) REVERT: C 557 LEU cc_start: 0.8801 (mm) cc_final: 0.8481 (mm) REVERT: C 566 LYS cc_start: 0.8621 (pttp) cc_final: 0.8201 (pttp) REVERT: C 584 HIS cc_start: 0.8473 (m90) cc_final: 0.8121 (m90) REVERT: C 590 LYS cc_start: 0.8447 (tttt) cc_final: 0.8105 (tttt) REVERT: C 606 LEU cc_start: 0.8684 (mp) cc_final: 0.8437 (mp) REVERT: D 18 ASP cc_start: 0.6142 (m-30) cc_final: 0.5859 (m-30) REVERT: D 78 ASN cc_start: 0.8867 (t0) cc_final: 0.8260 (t0) REVERT: D 99 MET cc_start: 0.6985 (ttm) cc_final: 0.6367 (ttm) REVERT: D 103 HIS cc_start: 0.6314 (m-70) cc_final: 0.5984 (m90) REVERT: D 140 LEU cc_start: 0.8993 (tt) cc_final: 0.8793 (tt) outliers start: 6 outliers final: 1 residues processed: 453 average time/residue: 0.2956 time to fit residues: 183.5827 Evaluate side-chains 399 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 397 time to evaluate : 1.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 91 optimal weight: 0.0570 chunk 128 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.2980 chunk 154 optimal weight: 6.9990 chunk 73 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 387 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.123233 restraints weight = 29786.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127600 restraints weight = 17156.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130557 restraints weight = 11204.606| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14205 Z= 0.150 Angle : 0.676 14.725 19562 Z= 0.357 Chirality : 0.041 0.181 2195 Planarity : 0.005 0.053 2244 Dihedral : 21.073 169.199 2554 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.66 % Favored : 91.27 % Rotamer: Outliers : 0.37 % Allowed : 4.87 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.22), residues: 1535 helix: 0.01 (0.21), residues: 587 sheet: -0.52 (0.35), residues: 240 loop : -1.64 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 363 HIS 0.006 0.001 HIS C 60 PHE 0.018 0.001 PHE A 589 TYR 0.023 0.002 TYR A 41 ARG 0.006 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 580) hydrogen bonds : angle 5.20331 ( 1605) covalent geometry : bond 0.00314 (14204) covalent geometry : angle 0.67559 (19562) Misc. bond : bond 0.00104 ( 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 441 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 436 time to evaluate : 1.278 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: 0.9093 (mttt) cc_final: 0.8708 (mttp) REVERT: A 66 PHE cc_start: 0.7285 (m-80) cc_final: 0.6958 (m-80) REVERT: A 119 ASP cc_start: 0.8636 (p0) cc_final: 0.8410 (p0) REVERT: A 157 ASP cc_start: 0.9041 (m-30) cc_final: 0.8341 (t0) REVERT: A 181 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8312 (ttp80) REVERT: A 226 VAL cc_start: 0.8742 (p) cc_final: 0.8403 (p) REVERT: A 231 LYS cc_start: 0.8981 (mptt) cc_final: 0.8712 (mptt) REVERT: A 236 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8532 (tppt) REVERT: A 246 LYS cc_start: 0.7357 (tmtt) cc_final: 0.7120 (tptp) REVERT: A 255 LEU cc_start: 0.7726 (mt) cc_final: 0.7289 (mm) REVERT: A 260 ASP cc_start: 0.7707 (p0) cc_final: 0.7454 (p0) REVERT: A 290 ARG cc_start: 0.8404 (ppt170) cc_final: 0.7812 (ppt170) REVERT: A 293 LYS cc_start: 0.7956 (pttm) cc_final: 0.7312 (pttm) REVERT: A 305 GLU cc_start: 0.8650 (tt0) cc_final: 0.7896 (tp30) REVERT: A 316 MET cc_start: 0.7035 (tmm) cc_final: 0.6688 (tmm) REVERT: A 320 HIS cc_start: 0.7165 (t-90) cc_final: 0.6568 (t-90) REVERT: A 323 GLN cc_start: 0.8362 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 324 THR cc_start: 0.8146 (t) cc_final: 0.7882 (t) REVERT: A 346 GLU cc_start: 0.7777 (mp0) cc_final: 0.7430 (mp0) REVERT: A 351 LYS cc_start: 0.8589 (tttp) cc_final: 0.8226 (mmtm) REVERT: A 355 ARG cc_start: 0.8410 (tpm170) cc_final: 0.7735 (tpm170) REVERT: A 368 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8450 (mtpt) REVERT: A 369 ARG cc_start: 0.9099 (ptm-80) cc_final: 0.8692 (ptm-80) REVERT: A 370 LEU cc_start: 0.8863 (tt) cc_final: 0.8384 (tt) REVERT: A 380 LYS cc_start: 0.8261 (ttpt) cc_final: 0.8048 (ttmt) REVERT: A 406 TRP cc_start: 0.8816 (t60) cc_final: 0.8442 (t60) REVERT: A 409 TYR cc_start: 0.8665 (t80) cc_final: 0.8231 (t80) REVERT: A 426 TYR cc_start: 0.7037 (p90) cc_final: 0.6680 (p90) REVERT: A 489 ASN cc_start: 0.7121 (p0) cc_final: 0.6807 (p0) REVERT: A 505 LYS cc_start: 0.9219 (tmtt) cc_final: 0.8827 (tmtt) REVERT: A 516 VAL cc_start: 0.8880 (m) cc_final: 0.8211 (p) REVERT: A 520 ASN cc_start: 0.8674 (m-40) cc_final: 0.8316 (m-40) REVERT: A 525 ASN cc_start: 0.6784 (m-40) cc_final: 0.6166 (m110) REVERT: A 565 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 603 MET cc_start: 0.8477 (mtm) cc_final: 0.8229 (mtm) REVERT: B 136 LYS cc_start: 0.7578 (mmpt) cc_final: 0.6997 (mmpt) REVERT: C 15 GLN cc_start: 0.8336 (pp30) cc_final: 0.8127 (pp30) REVERT: C 53 LYS cc_start: 0.7566 (mppt) cc_final: 0.6763 (mppt) REVERT: C 71 ASN cc_start: 0.7612 (m110) cc_final: 0.7348 (m110) REVERT: C 95 LYS cc_start: 0.9090 (mppt) cc_final: 0.8580 (mppt) REVERT: C 128 GLU cc_start: 0.7523 (mt-10) cc_final: 0.6926 (mt-10) REVERT: C 137 MET cc_start: 0.7383 (pmm) cc_final: 0.7130 (ptp) REVERT: C 139 LYS cc_start: 0.7455 (tmmt) cc_final: 0.6965 (ptmm) REVERT: C 144 GLU cc_start: 0.7070 (tp30) cc_final: 0.6707 (tp30) REVERT: C 164 MET cc_start: 0.8600 (ppp) cc_final: 0.8386 (ppp) REVERT: C 199 TYR cc_start: 0.7949 (t80) cc_final: 0.7657 (t80) REVERT: C 204 TYR cc_start: 0.7668 (m-80) cc_final: 0.7359 (m-10) REVERT: C 232 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7593 (mp) REVERT: C 236 LYS cc_start: 0.8645 (mppt) cc_final: 0.8048 (mppt) REVERT: C 262 VAL cc_start: 0.8849 (m) cc_final: 0.8621 (p) REVERT: C 267 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.7564 (ptm-80) REVERT: C 281 LYS cc_start: 0.6882 (mmmt) cc_final: 0.6602 (mmmt) REVERT: C 292 GLU cc_start: 0.8597 (pm20) cc_final: 0.8392 (pm20) REVERT: C 301 LEU cc_start: 0.8447 (tp) cc_final: 0.8076 (tp) REVERT: C 302 ASN cc_start: 0.8371 (t0) cc_final: 0.8056 (m-40) REVERT: C 305 GLU cc_start: 0.8087 (tp30) cc_final: 0.7842 (tp30) REVERT: C 308 ARG cc_start: 0.8677 (ttp-170) cc_final: 0.8201 (ttm-80) REVERT: C 323 GLN cc_start: 0.8727 (mt0) cc_final: 0.8432 (mm-40) REVERT: C 351 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8784 (tttm) REVERT: C 357 GLN cc_start: 0.7921 (tt0) cc_final: 0.7120 (tt0) REVERT: C 365 ASP cc_start: 0.8003 (p0) cc_final: 0.7670 (p0) REVERT: C 368 LYS cc_start: 0.9079 (ttmm) cc_final: 0.8848 (ttmm) REVERT: C 369 ARG cc_start: 0.8444 (mmp-170) cc_final: 0.8209 (mmp-170) REVERT: C 398 GLU cc_start: 0.7996 (tt0) cc_final: 0.7254 (tt0) REVERT: C 415 HIS cc_start: 0.7946 (t-90) cc_final: 0.7654 (t-90) REVERT: C 438 GLU cc_start: 0.8011 (mm-30) cc_final: 0.7406 (mp0) REVERT: C 442 CYS cc_start: 0.6656 (p) cc_final: 0.6088 (m) REVERT: C 449 SER cc_start: 0.8672 (t) cc_final: 0.8465 (t) REVERT: C 476 PHE cc_start: 0.7938 (m-80) cc_final: 0.7602 (m-80) REVERT: C 503 MET cc_start: 0.8276 (tpp) cc_final: 0.7962 (tpp) REVERT: C 504 GLU cc_start: 0.8568 (tp30) cc_final: 0.8125 (tp30) REVERT: C 557 LEU cc_start: 0.8804 (mm) cc_final: 0.8459 (mm) REVERT: C 566 LYS cc_start: 0.8652 (pttp) cc_final: 0.8269 (pttp) REVERT: C 584 HIS cc_start: 0.8479 (m90) cc_final: 0.8145 (m90) REVERT: C 590 LYS cc_start: 0.8503 (tttt) cc_final: 0.8206 (tttt) REVERT: C 603 MET cc_start: 0.7594 (mtt) cc_final: 0.7367 (mtt) REVERT: C 606 LEU cc_start: 0.8696 (mp) cc_final: 0.8425 (mp) REVERT: D 78 ASN cc_start: 0.8937 (t0) cc_final: 0.8411 (t0) REVERT: D 99 MET cc_start: 0.7037 (ttm) cc_final: 0.6826 (ttm) REVERT: D 103 HIS cc_start: 0.6465 (m-70) cc_final: 0.6175 (m90) REVERT: D 140 LEU cc_start: 0.8992 (tt) cc_final: 0.8761 (tt) REVERT: D 159 GLU cc_start: 0.8336 (mp0) cc_final: 0.8104 (mp0) outliers start: 5 outliers final: 1 residues processed: 437 average time/residue: 0.2928 time to fit residues: 175.9961 Evaluate side-chains 386 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 93 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 0.0070 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN C 48 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 573 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.150621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.116583 restraints weight = 30168.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120802 restraints weight = 17404.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.123710 restraints weight = 11350.925| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14205 Z= 0.233 Angle : 0.727 10.064 19562 Z= 0.394 Chirality : 0.044 0.183 2195 Planarity : 0.005 0.050 2244 Dihedral : 21.168 170.322 2554 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.06 % Favored : 90.88 % Rotamer: Outliers : 0.45 % Allowed : 5.24 % Favored : 94.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1535 helix: -0.17 (0.20), residues: 587 sheet: -0.68 (0.35), residues: 233 loop : -1.86 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 363 HIS 0.010 0.001 HIS A 60 PHE 0.039 0.002 PHE A 589 TYR 0.028 0.002 TYR A 41 ARG 0.008 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.05077 ( 580) hydrogen bonds : angle 5.42821 ( 1605) covalent geometry : bond 0.00471 (14204) covalent geometry : angle 0.72724 (19562) Misc. bond : bond 0.00183 ( 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 468 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 462 time to evaluate : 1.410 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: 0.9165 (mttt) cc_final: 0.8876 (mttp) REVERT: A 6 MET cc_start: 0.6413 (tmm) cc_final: 0.6189 (tmm) REVERT: A 55 THR cc_start: 0.7152 (p) cc_final: 0.6926 (p) REVERT: A 65 ASP cc_start: 0.8602 (t70) cc_final: 0.8277 (t0) REVERT: A 66 PHE cc_start: 0.7314 (m-80) cc_final: 0.7053 (m-80) REVERT: A 119 ASP cc_start: 0.8745 (p0) cc_final: 0.8507 (p0) REVERT: A 226 VAL cc_start: 0.8824 (p) cc_final: 0.8510 (p) REVERT: A 231 LYS cc_start: 0.9028 (mptt) cc_final: 0.8752 (mptt) REVERT: A 246 LYS cc_start: 0.7409 (tmtt) cc_final: 0.7037 (tmtt) REVERT: A 255 LEU cc_start: 0.7880 (mt) cc_final: 0.7333 (mm) REVERT: A 260 ASP cc_start: 0.7857 (p0) cc_final: 0.7544 (p0) REVERT: A 290 ARG cc_start: 0.8423 (ppt170) cc_final: 0.7837 (ppt170) REVERT: A 293 LYS cc_start: 0.7984 (pttm) cc_final: 0.7288 (pttm) REVERT: A 305 GLU cc_start: 0.8623 (tt0) cc_final: 0.7822 (tp30) REVERT: A 316 MET cc_start: 0.7209 (tmm) cc_final: 0.6996 (tmm) REVERT: A 320 HIS cc_start: 0.7457 (t-90) cc_final: 0.7186 (t-90) REVERT: A 330 THR cc_start: 0.8972 (m) cc_final: 0.8608 (p) REVERT: A 346 GLU cc_start: 0.7798 (mp0) cc_final: 0.7478 (mp0) REVERT: A 348 PHE cc_start: 0.8831 (t80) cc_final: 0.8463 (t80) REVERT: A 351 LYS cc_start: 0.8737 (tttp) cc_final: 0.8116 (mmtm) REVERT: A 368 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8494 (mtpt) REVERT: A 369 ARG cc_start: 0.9099 (ptm-80) cc_final: 0.8719 (ptm-80) REVERT: A 370 LEU cc_start: 0.8945 (tt) cc_final: 0.8480 (tt) REVERT: A 382 HIS cc_start: 0.7377 (t-90) cc_final: 0.7068 (t-90) REVERT: A 409 TYR cc_start: 0.8682 (t80) cc_final: 0.8205 (t80) REVERT: A 426 TYR cc_start: 0.7266 (p90) cc_final: 0.6802 (p90) REVERT: A 489 ASN cc_start: 0.7432 (p0) cc_final: 0.7109 (p0) REVERT: A 516 VAL cc_start: 0.8897 (m) cc_final: 0.8298 (p) REVERT: A 520 ASN cc_start: 0.8856 (m-40) cc_final: 0.8542 (m-40) REVERT: A 525 ASN cc_start: 0.7076 (m-40) cc_final: 0.6441 (m110) REVERT: A 530 GLU cc_start: 0.5251 (mp0) cc_final: 0.4780 (mp0) REVERT: A 565 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 128 LYS cc_start: 0.8463 (tttm) cc_final: 0.8015 (tttm) REVERT: B 136 LYS cc_start: 0.7931 (mmpt) cc_final: 0.7481 (mmpt) REVERT: B 143 ASN cc_start: 0.8401 (p0) cc_final: 0.8124 (p0) REVERT: C 15 GLN cc_start: 0.8433 (pp30) cc_final: 0.8037 (pp30) REVERT: C 17 ILE cc_start: 0.8735 (mt) cc_final: 0.8321 (mt) REVERT: C 30 LYS cc_start: 0.8129 (mttt) cc_final: 0.7896 (mttt) REVERT: C 32 LEU cc_start: 0.8004 (mt) cc_final: 0.7795 (mt) REVERT: C 39 HIS cc_start: 0.7392 (m-70) cc_final: 0.6966 (m-70) REVERT: C 53 LYS cc_start: 0.7390 (mppt) cc_final: 0.6607 (tppt) REVERT: C 71 ASN cc_start: 0.7663 (m110) cc_final: 0.7370 (m110) REVERT: C 95 LYS cc_start: 0.9139 (mppt) cc_final: 0.8720 (mppt) REVERT: C 128 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7131 (mt-10) REVERT: C 144 GLU cc_start: 0.7127 (tp30) cc_final: 0.6811 (tp30) REVERT: C 152 PHE cc_start: 0.7754 (p90) cc_final: 0.7491 (p90) REVERT: C 159 ASP cc_start: 0.7726 (t0) cc_final: 0.7174 (t0) REVERT: C 164 MET cc_start: 0.8658 (ppp) cc_final: 0.8413 (ppp) REVERT: C 204 TYR cc_start: 0.7760 (m-80) cc_final: 0.7452 (m-10) REVERT: C 232 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 236 LYS cc_start: 0.8752 (mppt) cc_final: 0.8156 (mppt) REVERT: C 244 GLN cc_start: 0.6247 (tp40) cc_final: 0.6002 (tp40) REVERT: C 267 ARG cc_start: 0.7945 (ptm-80) cc_final: 0.7582 (ptm-80) REVERT: C 301 LEU cc_start: 0.8278 (tp) cc_final: 0.8072 (tp) REVERT: C 302 ASN cc_start: 0.8244 (t0) cc_final: 0.7839 (m-40) REVERT: C 306 MET cc_start: 0.8075 (tmm) cc_final: 0.7592 (tmm) REVERT: C 307 LEU cc_start: 0.8891 (mt) cc_final: 0.8643 (mt) REVERT: C 308 ARG cc_start: 0.8663 (ttp-170) cc_final: 0.8266 (ttm-80) REVERT: C 323 GLN cc_start: 0.8812 (mt0) cc_final: 0.8445 (mm110) REVERT: C 344 TYR cc_start: 0.8998 (m-10) cc_final: 0.8744 (m-10) REVERT: C 351 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8814 (tttm) REVERT: C 357 GLN cc_start: 0.8167 (tt0) cc_final: 0.7088 (tt0) REVERT: C 365 ASP cc_start: 0.7985 (p0) cc_final: 0.7678 (p0) REVERT: C 410 GLU cc_start: 0.8382 (tt0) cc_final: 0.7986 (tt0) REVERT: C 430 THR cc_start: 0.7490 (t) cc_final: 0.7236 (t) REVERT: C 438 GLU cc_start: 0.7811 (mm-30) cc_final: 0.6950 (tp30) REVERT: C 445 LYS cc_start: 0.8233 (mttp) cc_final: 0.7740 (mttm) REVERT: C 476 PHE cc_start: 0.7978 (m-80) cc_final: 0.7718 (m-80) REVERT: C 494 LEU cc_start: 0.7976 (tp) cc_final: 0.7637 (tt) REVERT: C 504 GLU cc_start: 0.8615 (tp30) cc_final: 0.8204 (tp30) REVERT: C 523 GLN cc_start: 0.8392 (tt0) cc_final: 0.7691 (tp-100) REVERT: C 549 TYR cc_start: 0.7718 (m-80) cc_final: 0.7500 (m-80) REVERT: C 550 LYS cc_start: 0.8429 (mttt) cc_final: 0.8187 (mttt) REVERT: C 557 LEU cc_start: 0.9002 (mm) cc_final: 0.8718 (mm) REVERT: C 566 LYS cc_start: 0.8773 (pttp) cc_final: 0.8374 (pttp) REVERT: C 584 HIS cc_start: 0.8553 (m90) cc_final: 0.8245 (m90) REVERT: C 603 MET cc_start: 0.7738 (mtt) cc_final: 0.7500 (mtt) REVERT: C 606 LEU cc_start: 0.8737 (mp) cc_final: 0.8489 (mp) REVERT: D 78 ASN cc_start: 0.9213 (t0) cc_final: 0.8749 (t0) REVERT: D 99 MET cc_start: 0.6938 (ttm) cc_final: 0.6374 (ttm) REVERT: D 140 LEU cc_start: 0.8988 (tt) cc_final: 0.8754 (tt) REVERT: D 157 LEU cc_start: 0.8648 (mm) cc_final: 0.8370 (mm) REVERT: D 158 ILE cc_start: 0.9131 (tt) cc_final: 0.8898 (tt) outliers start: 6 outliers final: 1 residues processed: 463 average time/residue: 0.2841 time to fit residues: 183.0667 Evaluate side-chains 423 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 421 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 88 optimal weight: 4.9990 chunk 136 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 150 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 218 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.154321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119490 restraints weight = 30381.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123831 restraints weight = 17526.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.126801 restraints weight = 11606.040| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14205 Z= 0.157 Angle : 0.692 11.649 19562 Z= 0.367 Chirality : 0.043 0.167 2195 Planarity : 0.005 0.056 2244 Dihedral : 21.164 168.586 2554 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 0.22 % Allowed : 3.22 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.21), residues: 1535 helix: -0.11 (0.21), residues: 592 sheet: -0.60 (0.36), residues: 227 loop : -1.74 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP A 259 HIS 0.006 0.001 HIS A 506 PHE 0.038 0.002 PHE A 192 TYR 0.026 0.002 TYR A 41 ARG 0.008 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 580) hydrogen bonds : angle 5.22386 ( 1605) covalent geometry : bond 0.00330 (14204) covalent geometry : angle 0.69227 (19562) Misc. bond : bond 0.00121 ( 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 462 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 459 time to evaluate : 1.253 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 2 LYS cc_start: 0.9153 (mttt) cc_final: 0.8874 (mttp) REVERT: A 65 ASP cc_start: 0.8598 (t70) cc_final: 0.8265 (t0) REVERT: A 66 PHE cc_start: 0.7211 (m-80) cc_final: 0.6937 (m-80) REVERT: A 119 ASP cc_start: 0.8739 (p0) cc_final: 0.8537 (p0) REVERT: A 181 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8306 (ttp80) REVERT: A 226 VAL cc_start: 0.8800 (p) cc_final: 0.8433 (p) REVERT: A 231 LYS cc_start: 0.9000 (mptt) cc_final: 0.8709 (mptt) REVERT: A 236 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8581 (tppt) REVERT: A 246 LYS cc_start: 0.7240 (tmtt) cc_final: 0.6861 (tmtt) REVERT: A 255 LEU cc_start: 0.7890 (mt) cc_final: 0.7446 (mt) REVERT: A 260 ASP cc_start: 0.7896 (p0) cc_final: 0.7664 (p0) REVERT: A 290 ARG cc_start: 0.8401 (ppt170) cc_final: 0.7824 (ppt170) REVERT: A 293 LYS cc_start: 0.8007 (pttm) cc_final: 0.7339 (pttm) REVERT: A 305 GLU cc_start: 0.8614 (tt0) cc_final: 0.7863 (tp30) REVERT: A 323 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8201 (tm-30) REVERT: A 324 THR cc_start: 0.7955 (p) cc_final: 0.7663 (p) REVERT: A 328 LEU cc_start: 0.8179 (mt) cc_final: 0.7957 (mt) REVERT: A 330 THR cc_start: 0.8912 (m) cc_final: 0.8552 (p) REVERT: A 346 GLU cc_start: 0.7822 (mp0) cc_final: 0.7506 (mp0) REVERT: A 368 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8499 (mtpt) REVERT: A 369 ARG cc_start: 0.9129 (ptm-80) cc_final: 0.8697 (ptm-80) REVERT: A 370 LEU cc_start: 0.8976 (tt) cc_final: 0.8489 (tt) REVERT: A 382 HIS cc_start: 0.7505 (t-90) cc_final: 0.7170 (t-90) REVERT: A 409 TYR cc_start: 0.8693 (t80) cc_final: 0.8220 (t80) REVERT: A 426 TYR cc_start: 0.7182 (p90) cc_final: 0.6787 (p90) REVERT: A 441 THR cc_start: 0.7179 (t) cc_final: 0.6703 (m) REVERT: A 498 GLU cc_start: 0.8234 (mp0) cc_final: 0.7933 (mp0) REVERT: A 505 LYS cc_start: 0.9262 (tmtt) cc_final: 0.8873 (tmtt) REVERT: A 516 VAL cc_start: 0.8840 (m) cc_final: 0.8327 (p) REVERT: A 520 ASN cc_start: 0.8835 (m-40) cc_final: 0.8551 (m-40) REVERT: A 525 ASN cc_start: 0.6887 (m-40) cc_final: 0.6289 (m110) REVERT: A 560 ILE cc_start: 0.8247 (mt) cc_final: 0.7984 (pt) REVERT: A 565 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 569 ASN cc_start: 0.7030 (m110) cc_final: 0.6701 (m110) REVERT: B 106 CYS cc_start: 0.7478 (t) cc_final: 0.7264 (t) REVERT: B 128 LYS cc_start: 0.8385 (tttm) cc_final: 0.7956 (tttm) REVERT: B 136 LYS cc_start: 0.7748 (mmpt) cc_final: 0.7168 (mmpt) REVERT: C 15 GLN cc_start: 0.8409 (pp30) cc_final: 0.8147 (pp30) REVERT: C 30 LYS cc_start: 0.8157 (mttt) cc_final: 0.7897 (mttt) REVERT: C 32 LEU cc_start: 0.7885 (mt) cc_final: 0.7510 (mt) REVERT: C 39 HIS cc_start: 0.7372 (m-70) cc_final: 0.7092 (m-70) REVERT: C 41 TYR cc_start: 0.7162 (p90) cc_final: 0.6875 (p90) REVERT: C 53 LYS cc_start: 0.7102 (mppt) cc_final: 0.6353 (tppt) REVERT: C 71 ASN cc_start: 0.7696 (m110) cc_final: 0.7424 (m110) REVERT: C 84 GLN cc_start: 0.7875 (mp10) cc_final: 0.7427 (mp10) REVERT: C 95 LYS cc_start: 0.9093 (mppt) cc_final: 0.8685 (mppt) REVERT: C 98 MET cc_start: 0.7345 (ttt) cc_final: 0.6868 (ttt) REVERT: C 128 GLU cc_start: 0.7607 (mt-10) cc_final: 0.6963 (mt-10) REVERT: C 139 LYS cc_start: 0.7565 (tmmt) cc_final: 0.7105 (ptmm) REVERT: C 144 GLU cc_start: 0.7052 (tp30) cc_final: 0.6701 (tp30) REVERT: C 152 PHE cc_start: 0.7617 (p90) cc_final: 0.7360 (p90) REVERT: C 159 ASP cc_start: 0.7676 (t0) cc_final: 0.7063 (t0) REVERT: C 164 MET cc_start: 0.8591 (ppp) cc_final: 0.8334 (ppp) REVERT: C 199 TYR cc_start: 0.8058 (t80) cc_final: 0.7658 (t80) REVERT: C 204 TYR cc_start: 0.7744 (m-80) cc_final: 0.7426 (m-10) REVERT: C 236 LYS cc_start: 0.8726 (mppt) cc_final: 0.8145 (mppt) REVERT: C 244 GLN cc_start: 0.6258 (tp40) cc_final: 0.5964 (tp40) REVERT: C 263 ARG cc_start: 0.8335 (ptt180) cc_final: 0.6950 (ptt180) REVERT: C 273 PHE cc_start: 0.8080 (m-10) cc_final: 0.7802 (m-80) REVERT: C 301 LEU cc_start: 0.8308 (tp) cc_final: 0.7992 (tp) REVERT: C 302 ASN cc_start: 0.8128 (t0) cc_final: 0.7809 (m-40) REVERT: C 306 MET cc_start: 0.8063 (tmm) cc_final: 0.7549 (tmm) REVERT: C 307 LEU cc_start: 0.8914 (mt) cc_final: 0.8655 (mt) REVERT: C 308 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8153 (ttm-80) REVERT: C 351 LYS cc_start: 0.9058 (ttmm) cc_final: 0.8760 (tttm) REVERT: C 357 GLN cc_start: 0.8039 (tt0) cc_final: 0.7197 (tt0) REVERT: C 365 ASP cc_start: 0.7905 (p0) cc_final: 0.7613 (p0) REVERT: C 369 ARG cc_start: 0.8457 (mmp-170) cc_final: 0.8228 (mmp-170) REVERT: C 382 HIS cc_start: 0.8030 (t70) cc_final: 0.7799 (t-90) REVERT: C 410 GLU cc_start: 0.8352 (tt0) cc_final: 0.7965 (tt0) REVERT: C 430 THR cc_start: 0.7160 (t) cc_final: 0.6878 (t) REVERT: C 438 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7025 (tp30) REVERT: C 445 LYS cc_start: 0.8133 (mttp) cc_final: 0.7715 (mmtp) REVERT: C 449 SER cc_start: 0.8628 (t) cc_final: 0.8412 (t) REVERT: C 464 GLU cc_start: 0.7120 (mp0) cc_final: 0.6877 (mp0) REVERT: C 476 PHE cc_start: 0.7945 (m-80) cc_final: 0.7685 (m-80) REVERT: C 486 LYS cc_start: 0.6153 (mttt) cc_final: 0.5743 (mmtp) REVERT: C 494 LEU cc_start: 0.7944 (tp) cc_final: 0.7614 (tt) REVERT: C 504 GLU cc_start: 0.8544 (tp30) cc_final: 0.8048 (tp30) REVERT: C 549 TYR cc_start: 0.7726 (m-80) cc_final: 0.7418 (m-80) REVERT: C 550 LYS cc_start: 0.8386 (mttt) cc_final: 0.8156 (mttt) REVERT: C 557 LEU cc_start: 0.8959 (mm) cc_final: 0.8622 (mm) REVERT: C 566 LYS cc_start: 0.8754 (pttp) cc_final: 0.8364 (pttp) REVERT: C 584 HIS cc_start: 0.8509 (m90) cc_final: 0.8251 (m90) REVERT: C 603 MET cc_start: 0.7735 (mtt) cc_final: 0.7486 (mtt) REVERT: C 606 LEU cc_start: 0.8724 (mp) cc_final: 0.8478 (mp) REVERT: D 18 ASP cc_start: 0.6432 (m-30) cc_final: 0.6202 (m-30) REVERT: D 78 ASN cc_start: 0.9111 (t0) cc_final: 0.8416 (t0) REVERT: D 103 HIS cc_start: 0.6808 (m-70) cc_final: 0.6479 (m-70) REVERT: D 140 LEU cc_start: 0.8974 (tt) cc_final: 0.8762 (tt) REVERT: D 157 LEU cc_start: 0.8648 (mm) cc_final: 0.8361 (mm) outliers start: 3 outliers final: 0 residues processed: 459 average time/residue: 0.2753 time to fit residues: 176.1120 Evaluate side-chains 430 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 2 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 594 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 = 0.4103 r_free = 0.4103 target = 0.153846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118942 restraints weight = 30586.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123321 restraints weight = 17683.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126341 restraints weight = 11594.383| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3518 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= 0.160 Angle : 0.697 11.035 19562 Z= 0.370 Chirality : 0.043 0.170 2195 Planarity : 0.005 0.056 2244 Dihedral : 21.181 168.944 2554 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.34 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1535 helix: -0.06 (0.21), residues: 593 sheet: -0.67 (0.36), residues: 233 loop : -1.68 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 363 HIS 0.010 0.001 HIS C 415 PHE 0.061 0.002 PHE A 589 TYR 0.033 0.002 TYR A 41 ARG 0.009 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04477 ( 580) hydrogen bonds : angle 5.20182 ( 1605) covalent geometry : bond 0.00336 (14204) covalent geometry : angle 0.69711 (19562) Misc. bond : bond 0.00129 ( 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 455 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.455 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: A 2 LYS cc_start: 0.9134 (mttt) cc_final: 0.8869 (mttp) REVERT: A 65 ASP cc_start: 0.8590 (t70) cc_final: 0.8239 (t0) REVERT: A 66 PHE cc_start: 0.7235 (m-80) cc_final: 0.6968 (m-80) REVERT: A 181 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8267 (ttp80) REVERT: A 226 VAL cc_start: 0.8815 (p) cc_final: 0.8444 (p) REVERT: A 231 LYS cc_start: 0.9018 (mptt) cc_final: 0.8706 (mptt) REVERT: A 236 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8568 (tppt) REVERT: A 246 LYS cc_start: 0.7297 (tmtt) cc_final: 0.6915 (tmtt) REVERT: A 255 LEU cc_start: 0.7906 (mt) cc_final: 0.7427 (mt) REVERT: A 260 ASP cc_start: 0.7857 (p0) cc_final: 0.7581 (p0) REVERT: A 261 ARG cc_start: 0.9037 (mtp180) cc_final: 0.8811 (mtp180) REVERT: A 290 ARG cc_start: 0.8411 (ppt170) cc_final: 0.7847 (ppt170) REVERT: A 293 LYS cc_start: 0.8006 (pttm) cc_final: 0.7327 (pttm) REVERT: A 305 GLU cc_start: 0.8652 (tt0) cc_final: 0.7886 (tp30) REVERT: A 323 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8211 (tm-30) REVERT: A 324 THR cc_start: 0.7965 (p) cc_final: 0.7662 (p) REVERT: A 346 GLU cc_start: 0.7817 (mp0) cc_final: 0.7501 (mp0) REVERT: A 348 PHE cc_start: 0.8910 (t80) cc_final: 0.8541 (t80) REVERT: A 351 LYS cc_start: 0.8673 (mttm) cc_final: 0.8424 (ttmm) REVERT: A 368 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8501 (mtpt) REVERT: A 369 ARG cc_start: 0.9147 (ptm-80) cc_final: 0.8719 (ptm-80) REVERT: A 370 LEU cc_start: 0.9009 (tt) cc_final: 0.8582 (tt) REVERT: A 382 HIS cc_start: 0.7519 (t-90) cc_final: 0.7164 (t-90) REVERT: A 409 TYR cc_start: 0.8704 (t80) cc_final: 0.8254 (t80) REVERT: A 426 TYR cc_start: 0.7171 (p90) cc_final: 0.6799 (p90) REVERT: A 441 THR cc_start: 0.7145 (t) cc_final: 0.6698 (m) REVERT: A 482 LYS cc_start: 0.7795 (mmmm) cc_final: 0.7112 (mmmm) REVERT: A 498 GLU cc_start: 0.8202 (mp0) cc_final: 0.7968 (mp0) REVERT: A 502 LEU cc_start: 0.9065 (pp) cc_final: 0.8607 (pp) REVERT: A 505 LYS cc_start: 0.9268 (tmtt) cc_final: 0.8907 (tmtt) REVERT: A 516 VAL cc_start: 0.8831 (m) cc_final: 0.8307 (p) REVERT: A 520 ASN cc_start: 0.8852 (m-40) cc_final: 0.8512 (m-40) REVERT: A 525 ASN cc_start: 0.6972 (m-40) cc_final: 0.6373 (m110) REVERT: A 560 ILE cc_start: 0.8243 (mt) cc_final: 0.7929 (pt) REVERT: A 565 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7717 (mt-10) REVERT: A 569 ASN cc_start: 0.7079 (m110) cc_final: 0.6742 (m110) REVERT: B 128 LYS cc_start: 0.8417 (tttm) cc_final: 0.7996 (tttm) REVERT: B 136 LYS cc_start: 0.7852 (mmpt) cc_final: 0.7201 (mmpt) REVERT: C 15 GLN cc_start: 0.8452 (pp30) cc_final: 0.8198 (pp30) REVERT: C 30 LYS cc_start: 0.8197 (mttt) cc_final: 0.7939 (mttt) REVERT: C 32 LEU cc_start: 0.7919 (mt) cc_final: 0.7580 (mt) REVERT: C 41 TYR cc_start: 0.7171 (p90) cc_final: 0.6895 (p90) REVERT: C 53 LYS cc_start: 0.7061 (mppt) cc_final: 0.6322 (tppt) REVERT: C 71 ASN cc_start: 0.7710 (m110) cc_final: 0.7431 (m110) REVERT: C 84 GLN cc_start: 0.7926 (mp10) cc_final: 0.7443 (mp10) REVERT: C 89 LYS cc_start: 0.8359 (mppt) cc_final: 0.8060 (mppt) REVERT: C 95 LYS cc_start: 0.9089 (mppt) cc_final: 0.8676 (mppt) REVERT: C 98 MET cc_start: 0.7466 (ttt) cc_final: 0.6934 (ttt) REVERT: C 125 ILE cc_start: 0.7619 (mm) cc_final: 0.7370 (mm) REVERT: C 128 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7071 (mt-10) REVERT: C 144 GLU cc_start: 0.7120 (tp30) cc_final: 0.6767 (tp30) REVERT: C 152 PHE cc_start: 0.7499 (p90) cc_final: 0.7274 (p90) REVERT: C 159 ASP cc_start: 0.7652 (t0) cc_final: 0.6915 (t0) REVERT: C 164 MET cc_start: 0.8606 (ppp) cc_final: 0.8338 (ppp) REVERT: C 199 TYR cc_start: 0.8042 (t80) cc_final: 0.7649 (t80) REVERT: C 204 TYR cc_start: 0.7772 (m-80) cc_final: 0.7443 (m-10) REVERT: C 218 GLN cc_start: 0.7407 (mt0) cc_final: 0.6972 (mt0) REVERT: C 225 CYS cc_start: 0.8542 (m) cc_final: 0.8339 (m) REVERT: C 236 LYS cc_start: 0.8746 (mppt) cc_final: 0.8185 (mppt) REVERT: C 244 GLN cc_start: 0.6212 (tp40) cc_final: 0.5900 (tp40) REVERT: C 263 ARG cc_start: 0.8310 (ptt180) cc_final: 0.6992 (ptt180) REVERT: C 267 ARG cc_start: 0.7982 (ppt170) cc_final: 0.7396 (ppt170) REVERT: C 273 PHE cc_start: 0.8108 (m-10) cc_final: 0.7840 (m-80) REVERT: C 292 GLU cc_start: 0.8665 (pm20) cc_final: 0.8388 (pm20) REVERT: C 301 LEU cc_start: 0.8381 (tp) cc_final: 0.7957 (tp) REVERT: C 302 ASN cc_start: 0.8265 (t0) cc_final: 0.7791 (m110) REVERT: C 306 MET cc_start: 0.8065 (tmm) cc_final: 0.7637 (tmm) REVERT: C 307 LEU cc_start: 0.8916 (mt) cc_final: 0.8667 (mt) REVERT: C 316 MET cc_start: 0.7327 (mtt) cc_final: 0.7025 (mtt) REVERT: C 351 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8688 (tttm) REVERT: C 357 GLN cc_start: 0.8022 (tt0) cc_final: 0.7218 (tt0) REVERT: C 365 ASP cc_start: 0.7920 (p0) cc_final: 0.7662 (p0) REVERT: C 369 ARG cc_start: 0.8438 (mmp-170) cc_final: 0.8227 (mmp-170) REVERT: C 382 HIS cc_start: 0.8044 (t70) cc_final: 0.7810 (t-90) REVERT: C 410 GLU cc_start: 0.8352 (tt0) cc_final: 0.7949 (tt0) REVERT: C 464 GLU cc_start: 0.7088 (mp0) cc_final: 0.6870 (mp0) REVERT: C 476 PHE cc_start: 0.7993 (m-80) cc_final: 0.7712 (m-80) REVERT: C 486 LYS cc_start: 0.6167 (mttt) cc_final: 0.5737 (mmtp) REVERT: C 494 LEU cc_start: 0.8044 (tp) cc_final: 0.7722 (tt) REVERT: C 504 GLU cc_start: 0.8477 (tp30) cc_final: 0.8010 (tp30) REVERT: C 549 TYR cc_start: 0.7715 (m-80) cc_final: 0.7395 (m-80) REVERT: C 550 LYS cc_start: 0.8387 (mttt) cc_final: 0.8176 (mttt) REVERT: C 557 LEU cc_start: 0.8975 (mm) cc_final: 0.8645 (mm) REVERT: C 566 LYS cc_start: 0.8777 (pttp) cc_final: 0.8368 (pttp) REVERT: C 582 LEU cc_start: 0.8912 (mt) cc_final: 0.8691 (mt) REVERT: C 584 HIS cc_start: 0.8511 (m90) cc_final: 0.8241 (m90) REVERT: C 603 MET cc_start: 0.7750 (mtt) cc_final: 0.7483 (mtt) REVERT: C 606 LEU cc_start: 0.8713 (mp) cc_final: 0.8464 (mp) REVERT: D 18 ASP cc_start: 0.6495 (m-30) cc_final: 0.6035 (m-30) REVERT: D 78 ASN cc_start: 0.9103 (t0) cc_final: 0.8418 (t0) REVERT: D 87 GLU cc_start: 0.8123 (tp30) cc_final: 0.7749 (mm-30) REVERT: D 89 GLN cc_start: 0.8905 (mm110) cc_final: 0.8704 (mm110) REVERT: D 103 HIS cc_start: 0.6813 (m-70) cc_final: 0.6508 (m-70) REVERT: D 114 MET cc_start: 0.8572 (tmm) cc_final: 0.7974 (tmm) REVERT: D 140 LEU cc_start: 0.8950 (tt) cc_final: 0.8749 (tt) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2848 time to fit residues: 179.2532 Evaluate side-chains 415 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 415 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 0.0870 chunk 89 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN C 343 HIS ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** 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 = 0.4119 r_free = 0.4119 target = 0.154876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119851 restraints weight = 30635.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.124194 restraints weight = 17758.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.127209 restraints weight = 11794.638| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14205 Z= 0.151 Angle : 0.700 10.522 19562 Z= 0.370 Chirality : 0.043 0.166 2195 Planarity : 0.005 0.056 2244 Dihedral : 21.178 168.822 2554 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.01 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.21), residues: 1535 helix: 0.00 (0.21), residues: 592 sheet: -0.70 (0.36), residues: 227 loop : -1.65 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP A 259 HIS 0.009 0.001 HIS A 506 PHE 0.024 0.001 PHE A 589 TYR 0.020 0.002 TYR A 595 ARG 0.009 0.001 ARG C 591 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 580) hydrogen bonds : angle 5.17156 ( 1605) covalent geometry : bond 0.00326 (14204) covalent geometry : angle 0.70021 (19562) Misc. bond : bond 0.00122 ( 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 461 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.290 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 2 LYS cc_start: 0.9107 (mttt) cc_final: 0.8876 (mttp) REVERT: A 65 ASP cc_start: 0.8586 (t70) cc_final: 0.8212 (t0) REVERT: A 66 PHE cc_start: 0.7236 (m-80) cc_final: 0.6903 (m-80) REVERT: A 181 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8163 (ttp80) REVERT: A 231 LYS cc_start: 0.9012 (mptt) cc_final: 0.8707 (mptt) REVERT: A 246 LYS cc_start: 0.7271 (tmtt) cc_final: 0.6881 (tmtt) REVERT: A 255 LEU cc_start: 0.7889 (mt) cc_final: 0.7394 (mt) REVERT: A 260 ASP cc_start: 0.7944 (p0) cc_final: 0.7692 (p0) REVERT: A 290 ARG cc_start: 0.8434 (ppt170) cc_final: 0.8151 (ppt170) REVERT: A 293 LYS cc_start: 0.7998 (pttm) cc_final: 0.7346 (pttm) REVERT: A 305 GLU cc_start: 0.8647 (tt0) cc_final: 0.7863 (tp30) REVERT: A 328 LEU cc_start: 0.8189 (mt) cc_final: 0.7973 (mt) REVERT: A 346 GLU cc_start: 0.7823 (mp0) cc_final: 0.7519 (mp0) REVERT: A 348 PHE cc_start: 0.8917 (t80) cc_final: 0.8538 (t80) REVERT: A 351 LYS cc_start: 0.8653 (mttm) cc_final: 0.7820 (ttmm) REVERT: A 355 ARG cc_start: 0.8483 (ttm110) cc_final: 0.7862 (ttm110) REVERT: A 366 THR cc_start: 0.8557 (p) cc_final: 0.8350 (p) REVERT: A 368 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8497 (mtpt) REVERT: A 369 ARG cc_start: 0.9147 (ptm-80) cc_final: 0.8738 (ptm-80) REVERT: A 370 LEU cc_start: 0.9028 (tt) cc_final: 0.8561 (tt) REVERT: A 382 HIS cc_start: 0.7583 (t-90) cc_final: 0.7202 (t-90) REVERT: A 409 TYR cc_start: 0.8688 (t80) cc_final: 0.8229 (t80) REVERT: A 426 TYR cc_start: 0.7139 (p90) cc_final: 0.6778 (p90) REVERT: A 482 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7127 (mmmm) REVERT: A 498 GLU cc_start: 0.8193 (mp0) cc_final: 0.7973 (mp0) REVERT: A 502 LEU cc_start: 0.9061 (pp) cc_final: 0.8604 (pp) REVERT: A 505 LYS cc_start: 0.9267 (tmtt) cc_final: 0.8909 (tmtt) REVERT: A 516 VAL cc_start: 0.8834 (m) cc_final: 0.8284 (p) REVERT: A 520 ASN cc_start: 0.8864 (m-40) cc_final: 0.8500 (m-40) REVERT: A 525 ASN cc_start: 0.7041 (m-40) cc_final: 0.6415 (m110) REVERT: A 560 ILE cc_start: 0.8246 (mt) cc_final: 0.7907 (pt) REVERT: A 565 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7695 (mt-10) REVERT: A 569 ASN cc_start: 0.7098 (m110) cc_final: 0.6745 (m110) REVERT: B 106 CYS cc_start: 0.7565 (t) cc_final: 0.7316 (t) REVERT: B 128 LYS cc_start: 0.8425 (tttm) cc_final: 0.7981 (tttm) REVERT: B 136 LYS cc_start: 0.7801 (mmpt) cc_final: 0.7179 (mmpt) REVERT: C 15 GLN cc_start: 0.8502 (pp30) cc_final: 0.8298 (pp30) REVERT: C 30 LYS cc_start: 0.8213 (mttt) cc_final: 0.7943 (mttt) REVERT: C 32 LEU cc_start: 0.7889 (mt) cc_final: 0.7540 (mt) REVERT: C 41 TYR cc_start: 0.7200 (p90) cc_final: 0.6919 (p90) REVERT: C 53 LYS cc_start: 0.6768 (mppt) cc_final: 0.6221 (mppt) REVERT: C 71 ASN cc_start: 0.7697 (m110) cc_final: 0.7415 (m110) REVERT: C 84 GLN cc_start: 0.7938 (mp10) cc_final: 0.7439 (mp10) REVERT: C 89 LYS cc_start: 0.8366 (mppt) cc_final: 0.8059 (mppt) REVERT: C 95 LYS cc_start: 0.9083 (mppt) cc_final: 0.8680 (mppt) REVERT: C 98 MET cc_start: 0.7431 (ttt) cc_final: 0.6880 (ttt) REVERT: C 128 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7059 (mt-10) REVERT: C 144 GLU cc_start: 0.7140 (tp30) cc_final: 0.6811 (tp30) REVERT: C 159 ASP cc_start: 0.7611 (t0) cc_final: 0.6978 (t0) REVERT: C 164 MET cc_start: 0.8618 (ppp) cc_final: 0.8344 (ppp) REVERT: C 199 TYR cc_start: 0.7987 (t80) cc_final: 0.7572 (t80) REVERT: C 204 TYR cc_start: 0.7771 (m-80) cc_final: 0.7441 (m-10) REVERT: C 218 GLN cc_start: 0.7404 (mt0) cc_final: 0.6900 (mt0) REVERT: C 222 LEU cc_start: 0.7965 (tp) cc_final: 0.7719 (tp) REVERT: C 225 CYS cc_start: 0.8518 (m) cc_final: 0.8306 (m) REVERT: C 236 LYS cc_start: 0.8743 (mppt) cc_final: 0.8176 (mppt) REVERT: C 244 GLN cc_start: 0.6221 (tp-100) cc_final: 0.5985 (tp-100) REVERT: C 263 ARG cc_start: 0.8293 (ptt180) cc_final: 0.6986 (ptt180) REVERT: C 267 ARG cc_start: 0.7997 (ppt170) cc_final: 0.7419 (ppt170) REVERT: C 273 PHE cc_start: 0.8153 (m-10) cc_final: 0.7861 (m-80) REVERT: C 292 GLU cc_start: 0.8647 (pm20) cc_final: 0.8271 (pm20) REVERT: C 302 ASN cc_start: 0.8314 (t0) cc_final: 0.7905 (m110) REVERT: C 306 MET cc_start: 0.8083 (tmm) cc_final: 0.7614 (tmm) REVERT: C 307 LEU cc_start: 0.8915 (mt) cc_final: 0.8683 (mt) REVERT: C 316 MET cc_start: 0.7376 (mtt) cc_final: 0.7075 (mtt) REVERT: C 351 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8674 (tttm) REVERT: C 357 GLN cc_start: 0.8065 (tt0) cc_final: 0.7330 (tt0) REVERT: C 365 ASP cc_start: 0.7923 (p0) cc_final: 0.7669 (p0) REVERT: C 369 ARG cc_start: 0.8459 (mmp-170) cc_final: 0.8207 (mmp-170) REVERT: C 410 GLU cc_start: 0.8348 (tt0) cc_final: 0.7969 (tt0) REVERT: C 445 LYS cc_start: 0.8230 (mttm) cc_final: 0.7964 (mmtp) REVERT: C 449 SER cc_start: 0.8610 (t) cc_final: 0.8400 (t) REVERT: C 454 GLU cc_start: 0.8011 (pt0) cc_final: 0.7794 (pt0) REVERT: C 464 GLU cc_start: 0.7086 (mp0) cc_final: 0.6815 (mp0) REVERT: C 494 LEU cc_start: 0.8106 (tp) cc_final: 0.7797 (tt) REVERT: C 504 GLU cc_start: 0.8439 (tp30) cc_final: 0.7981 (tp30) REVERT: C 549 TYR cc_start: 0.7700 (m-80) cc_final: 0.7353 (m-80) REVERT: C 550 LYS cc_start: 0.8357 (mttt) cc_final: 0.8138 (mttt) REVERT: C 557 LEU cc_start: 0.8982 (mm) cc_final: 0.8642 (mm) REVERT: C 566 LYS cc_start: 0.8757 (pttp) cc_final: 0.8345 (pttp) REVERT: C 582 LEU cc_start: 0.8924 (mt) cc_final: 0.8708 (mt) REVERT: C 584 HIS cc_start: 0.8535 (m90) cc_final: 0.8264 (m90) REVERT: C 591 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8094 (mmm160) REVERT: C 603 MET cc_start: 0.7728 (mtt) cc_final: 0.7490 (mtt) REVERT: C 606 LEU cc_start: 0.8718 (mp) cc_final: 0.8494 (mp) REVERT: D 18 ASP cc_start: 0.6548 (m-30) cc_final: 0.5972 (m-30) REVERT: D 78 ASN cc_start: 0.9071 (t0) cc_final: 0.8382 (t0) REVERT: D 87 GLU cc_start: 0.8102 (tp30) cc_final: 0.7705 (mm-30) REVERT: D 103 HIS cc_start: 0.6828 (m-70) cc_final: 0.6518 (m-70) REVERT: D 157 LEU cc_start: 0.8622 (mm) cc_final: 0.8379 (mm) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.2673 time to fit residues: 172.9811 Evaluate side-chains 430 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 55 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** 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 = 0.4117 r_free = 0.4117 target = 0.154732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.119618 restraints weight = 30354.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123977 restraints weight = 17635.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.126992 restraints weight = 11608.771| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3927 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= 0.155 Angle : 0.719 13.522 19562 Z= 0.378 Chirality : 0.043 0.168 2195 Planarity : 0.005 0.073 2244 Dihedral : 21.187 169.247 2554 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.34 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1535 helix: -0.07 (0.21), residues: 592 sheet: -0.54 (0.34), residues: 248 loop : -1.75 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 259 HIS 0.008 0.001 HIS A 506 PHE 0.035 0.002 PHE A 589 TYR 0.028 0.002 TYR A 41 ARG 0.010 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 580) hydrogen bonds : angle 5.21815 ( 1605) covalent geometry : bond 0.00332 (14204) covalent geometry : angle 0.71884 (19562) Misc. bond : bond 0.00116 ( 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 454 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9134 (mttt) cc_final: 0.8915 (mttp) REVERT: A 62 MET cc_start: 0.6193 (tmm) cc_final: 0.5951 (tmm) REVERT: A 65 ASP cc_start: 0.8601 (t70) cc_final: 0.8246 (t0) REVERT: A 66 PHE cc_start: 0.7229 (m-80) cc_final: 0.6898 (m-80) REVERT: A 90 LYS cc_start: 0.7987 (pptt) cc_final: 0.7367 (tmmt) REVERT: A 181 ARG cc_start: 0.8627 (ttp80) cc_final: 0.8228 (ttp80) REVERT: A 231 LYS cc_start: 0.9018 (mptt) cc_final: 0.8708 (mptt) REVERT: A 255 LEU cc_start: 0.7938 (mt) cc_final: 0.7594 (mt) REVERT: A 260 ASP cc_start: 0.8084 (p0) cc_final: 0.7853 (p0) REVERT: A 290 ARG cc_start: 0.8449 (ppt170) cc_final: 0.8142 (ppt170) REVERT: A 293 LYS cc_start: 0.8004 (pttm) cc_final: 0.7362 (pttm) REVERT: A 305 GLU cc_start: 0.8656 (tt0) cc_final: 0.7894 (tp30) REVERT: A 346 GLU cc_start: 0.7821 (mp0) cc_final: 0.7525 (mp0) REVERT: A 348 PHE cc_start: 0.8924 (t80) cc_final: 0.8477 (t80) REVERT: A 351 LYS cc_start: 0.8697 (mttm) cc_final: 0.7590 (mttm) REVERT: A 355 ARG cc_start: 0.8506 (ttm110) cc_final: 0.7799 (ttm110) REVERT: A 368 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8515 (mtpt) REVERT: A 370 LEU cc_start: 0.8998 (tt) cc_final: 0.8779 (tt) REVERT: A 382 HIS cc_start: 0.7584 (t-90) cc_final: 0.7194 (t-90) REVERT: A 409 TYR cc_start: 0.8680 (t80) cc_final: 0.8237 (t80) REVERT: A 426 TYR cc_start: 0.7140 (p90) cc_final: 0.6776 (p90) REVERT: A 441 THR cc_start: 0.7101 (t) cc_final: 0.6652 (m) REVERT: A 482 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7109 (mmmm) REVERT: A 498 GLU cc_start: 0.8199 (mp0) cc_final: 0.7995 (mp0) REVERT: A 502 LEU cc_start: 0.9089 (pp) cc_final: 0.8612 (pp) REVERT: A 516 VAL cc_start: 0.8821 (m) cc_final: 0.8278 (p) REVERT: A 518 ILE cc_start: 0.8929 (mm) cc_final: 0.8679 (tp) REVERT: A 520 ASN cc_start: 0.8843 (m-40) cc_final: 0.8460 (m-40) REVERT: A 525 ASN cc_start: 0.7094 (m-40) cc_final: 0.6457 (m110) REVERT: A 560 ILE cc_start: 0.8242 (mt) cc_final: 0.7906 (pt) REVERT: A 565 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7572 (mt-10) REVERT: A 569 ASN cc_start: 0.7120 (m110) cc_final: 0.6805 (m110) REVERT: B 106 CYS cc_start: 0.7570 (t) cc_final: 0.7340 (t) REVERT: B 128 LYS cc_start: 0.8452 (tttm) cc_final: 0.7974 (tttm) REVERT: B 136 LYS cc_start: 0.7849 (mmpt) cc_final: 0.7415 (mmpt) REVERT: C 15 GLN cc_start: 0.8509 (pp30) cc_final: 0.8253 (pp30) REVERT: C 30 LYS cc_start: 0.8189 (mttt) cc_final: 0.7945 (mttt) REVERT: C 32 LEU cc_start: 0.7944 (mt) cc_final: 0.7617 (mt) REVERT: C 41 TYR cc_start: 0.7196 (p90) cc_final: 0.6958 (p90) REVERT: C 53 LYS cc_start: 0.6705 (mppt) cc_final: 0.6133 (mppt) REVERT: C 71 ASN cc_start: 0.7663 (m110) cc_final: 0.7384 (m110) REVERT: C 84 GLN cc_start: 0.7952 (mp10) cc_final: 0.7463 (mp10) REVERT: C 95 LYS cc_start: 0.9087 (mppt) cc_final: 0.8669 (mppt) REVERT: C 98 MET cc_start: 0.7480 (ttt) cc_final: 0.7007 (ttt) REVERT: C 128 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7111 (mt-10) REVERT: C 144 GLU cc_start: 0.7154 (tp30) cc_final: 0.6630 (tm-30) REVERT: C 159 ASP cc_start: 0.7594 (t0) cc_final: 0.6914 (t0) REVERT: C 164 MET cc_start: 0.8613 (ppp) cc_final: 0.8335 (ppp) REVERT: C 199 TYR cc_start: 0.7964 (t80) cc_final: 0.7583 (t80) REVERT: C 204 TYR cc_start: 0.7789 (m-80) cc_final: 0.7446 (m-10) REVERT: C 218 GLN cc_start: 0.7465 (mt0) cc_final: 0.6980 (mt0) REVERT: C 222 LEU cc_start: 0.7966 (tp) cc_final: 0.7708 (tp) REVERT: C 225 CYS cc_start: 0.8537 (m) cc_final: 0.8292 (m) REVERT: C 236 LYS cc_start: 0.8752 (mppt) cc_final: 0.8207 (mppt) REVERT: C 244 GLN cc_start: 0.6239 (tp-100) cc_final: 0.5987 (tp-100) REVERT: C 263 ARG cc_start: 0.8293 (ptt180) cc_final: 0.6953 (ptt180) REVERT: C 264 VAL cc_start: 0.7864 (m) cc_final: 0.7515 (p) REVERT: C 267 ARG cc_start: 0.7979 (ppt170) cc_final: 0.7450 (ppt170) REVERT: C 269 ILE cc_start: 0.8690 (mm) cc_final: 0.7008 (mm) REVERT: C 273 PHE cc_start: 0.8199 (m-10) cc_final: 0.7920 (m-80) REVERT: C 302 ASN cc_start: 0.8323 (t0) cc_final: 0.7885 (m110) REVERT: C 306 MET cc_start: 0.8138 (tmm) cc_final: 0.7348 (tmm) REVERT: C 308 ARG cc_start: 0.8503 (ttp-170) cc_final: 0.8167 (ttp-170) REVERT: C 316 MET cc_start: 0.7307 (mtt) cc_final: 0.7103 (mtt) REVERT: C 351 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8703 (tttm) REVERT: C 357 GLN cc_start: 0.8067 (tt0) cc_final: 0.7340 (tt0) REVERT: C 369 ARG cc_start: 0.8432 (mmp-170) cc_final: 0.8218 (mmp-170) REVERT: C 410 GLU cc_start: 0.8342 (tt0) cc_final: 0.7974 (tt0) REVERT: C 449 SER cc_start: 0.8604 (t) cc_final: 0.8401 (t) REVERT: C 464 GLU cc_start: 0.7041 (mp0) cc_final: 0.6794 (mp0) REVERT: C 494 LEU cc_start: 0.8148 (tp) cc_final: 0.7844 (tt) REVERT: C 504 GLU cc_start: 0.8432 (tp30) cc_final: 0.7989 (tp30) REVERT: C 536 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7478 (ttmt) REVERT: C 549 TYR cc_start: 0.7695 (m-80) cc_final: 0.7320 (m-80) REVERT: C 550 LYS cc_start: 0.8347 (mttt) cc_final: 0.8130 (mttt) REVERT: C 557 LEU cc_start: 0.8973 (mm) cc_final: 0.8610 (mm) REVERT: C 566 LYS cc_start: 0.8758 (pttp) cc_final: 0.8348 (pttp) REVERT: C 582 LEU cc_start: 0.8912 (mt) cc_final: 0.8628 (mt) REVERT: C 584 HIS cc_start: 0.8520 (m90) cc_final: 0.8242 (m90) REVERT: C 591 ARG cc_start: 0.8267 (mmm160) cc_final: 0.8044 (mmm160) REVERT: C 603 MET cc_start: 0.7704 (mtt) cc_final: 0.7474 (mtt) REVERT: C 606 LEU cc_start: 0.8723 (mp) cc_final: 0.8510 (mp) REVERT: D 18 ASP cc_start: 0.6446 (m-30) cc_final: 0.5978 (m-30) REVERT: D 78 ASN cc_start: 0.9063 (t0) cc_final: 0.8361 (t0) REVERT: D 87 GLU cc_start: 0.8151 (tp30) cc_final: 0.7858 (mm-30) REVERT: D 89 GLN cc_start: 0.8923 (mm110) cc_final: 0.8714 (mm110) REVERT: D 103 HIS cc_start: 0.6765 (m-70) cc_final: 0.6498 (m-70) REVERT: D 157 LEU cc_start: 0.8640 (mm) cc_final: 0.8332 (mm) REVERT: D 158 ILE cc_start: 0.8984 (tt) cc_final: 0.8734 (tt) REVERT: D 159 GLU cc_start: 0.8327 (mp0) cc_final: 0.8113 (mp0) outliers start: 0 outliers final: 0 residues processed: 454 average time/residue: 0.2670 time to fit residues: 169.8775 Evaluate side-chains 424 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS C 48 GLN ** C 360 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 = 0.4078 r_free = 0.4078 target = 0.151302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.116483 restraints weight = 29903.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.120802 restraints weight = 17447.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.123777 restraints weight = 11459.778| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14205 Z= 0.212 Angle : 0.760 13.076 19562 Z= 0.405 Chirality : 0.045 0.170 2195 Planarity : 0.005 0.069 2244 Dihedral : 21.242 170.592 2554 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.45 % Favored : 90.49 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.21), residues: 1535 helix: -0.23 (0.20), residues: 591 sheet: -0.85 (0.35), residues: 235 loop : -1.81 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 363 HIS 0.008 0.001 HIS C 360 PHE 0.036 0.002 PHE A 589 TYR 0.022 0.002 TYR C 199 ARG 0.012 0.001 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 580) hydrogen bonds : angle 5.43119 ( 1605) covalent geometry : bond 0.00436 (14204) covalent geometry : angle 0.75997 (19562) Misc. bond : bond 0.00149 ( 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 455 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.299 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 2 LYS cc_start: 0.9172 (mttt) cc_final: 0.8946 (mttp) REVERT: A 62 MET cc_start: 0.6336 (tmm) cc_final: 0.6092 (tmm) REVERT: A 65 ASP cc_start: 0.8663 (t70) cc_final: 0.8288 (t0) REVERT: A 66 PHE cc_start: 0.7334 (m-80) cc_final: 0.6978 (m-80) REVERT: A 90 LYS cc_start: 0.8000 (pptt) cc_final: 0.7251 (tmmt) REVERT: A 231 LYS cc_start: 0.9079 (mptt) cc_final: 0.8818 (mptt) REVERT: A 255 LEU cc_start: 0.7942 (mt) cc_final: 0.7686 (mt) REVERT: A 259 TRP cc_start: 0.8239 (t60) cc_final: 0.8005 (t60) REVERT: A 260 ASP cc_start: 0.8108 (p0) cc_final: 0.7873 (p0) REVERT: A 272 MET cc_start: 0.7688 (mtt) cc_final: 0.7480 (mtt) REVERT: A 276 MET cc_start: 0.7710 (tpt) cc_final: 0.7474 (tpt) REVERT: A 293 LYS cc_start: 0.8012 (pttm) cc_final: 0.7544 (pttm) REVERT: A 297 ARG cc_start: 0.6399 (ptm160) cc_final: 0.5887 (ptm160) REVERT: A 305 GLU cc_start: 0.8689 (tt0) cc_final: 0.7875 (tp30) REVERT: A 320 HIS cc_start: 0.7416 (t-90) cc_final: 0.7126 (t-90) REVERT: A 346 GLU cc_start: 0.7762 (mp0) cc_final: 0.7490 (mp0) REVERT: A 348 PHE cc_start: 0.8936 (t80) cc_final: 0.8542 (t80) REVERT: A 351 LYS cc_start: 0.8736 (mttm) cc_final: 0.7871 (mttm) REVERT: A 355 ARG cc_start: 0.8506 (ttm110) cc_final: 0.7926 (ttm110) REVERT: A 368 LYS cc_start: 0.8813 (mtpt) cc_final: 0.8482 (mtpt) REVERT: A 369 ARG cc_start: 0.9163 (ptm-80) cc_final: 0.8740 (ptm-80) REVERT: A 370 LEU cc_start: 0.9047 (tt) cc_final: 0.8581 (tt) REVERT: A 380 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8204 (ttmt) REVERT: A 382 HIS cc_start: 0.7745 (t-90) cc_final: 0.7265 (t-90) REVERT: A 409 TYR cc_start: 0.8683 (t80) cc_final: 0.8256 (t80) REVERT: A 426 TYR cc_start: 0.7182 (p90) cc_final: 0.6941 (p90) REVERT: A 482 LYS cc_start: 0.7789 (mmmm) cc_final: 0.7099 (mmmm) REVERT: A 489 ASN cc_start: 0.6717 (p0) cc_final: 0.6515 (p0) REVERT: A 516 VAL cc_start: 0.8880 (m) cc_final: 0.8340 (p) REVERT: A 518 ILE cc_start: 0.8937 (mm) cc_final: 0.8673 (tp) REVERT: A 520 ASN cc_start: 0.8851 (m-40) cc_final: 0.8464 (m-40) REVERT: A 525 ASN cc_start: 0.7240 (m-40) cc_final: 0.6644 (m110) REVERT: A 560 ILE cc_start: 0.8356 (mt) cc_final: 0.8022 (pt) REVERT: A 565 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7602 (mt-10) REVERT: A 569 ASN cc_start: 0.7225 (m110) cc_final: 0.6881 (m110) REVERT: B 106 CYS cc_start: 0.7572 (t) cc_final: 0.7304 (t) REVERT: B 128 LYS cc_start: 0.8495 (tttm) cc_final: 0.8031 (tttm) REVERT: B 136 LYS cc_start: 0.7809 (mmpt) cc_final: 0.7569 (mmpt) REVERT: C 15 GLN cc_start: 0.8611 (pp30) cc_final: 0.8310 (pp30) REVERT: C 30 LYS cc_start: 0.8181 (mttt) cc_final: 0.7942 (mttt) REVERT: C 32 LEU cc_start: 0.7884 (mt) cc_final: 0.7547 (mt) REVERT: C 41 TYR cc_start: 0.7278 (p90) cc_final: 0.7039 (p90) REVERT: C 53 LYS cc_start: 0.6718 (mppt) cc_final: 0.6131 (mppt) REVERT: C 71 ASN cc_start: 0.7644 (m110) cc_final: 0.7370 (m110) REVERT: C 84 GLN cc_start: 0.8002 (mp10) cc_final: 0.7493 (mp10) REVERT: C 95 LYS cc_start: 0.9098 (mppt) cc_final: 0.8652 (mppt) REVERT: C 98 MET cc_start: 0.7527 (ttt) cc_final: 0.7059 (ttt) REVERT: C 144 GLU cc_start: 0.7121 (tp30) cc_final: 0.6832 (tp30) REVERT: C 159 ASP cc_start: 0.7678 (t0) cc_final: 0.6990 (t0) REVERT: C 164 MET cc_start: 0.8660 (ppp) cc_final: 0.8309 (ppp) REVERT: C 171 ASP cc_start: 0.8555 (t70) cc_final: 0.8259 (t0) REVERT: C 204 TYR cc_start: 0.7876 (m-80) cc_final: 0.7546 (m-10) REVERT: C 218 GLN cc_start: 0.7406 (mt0) cc_final: 0.6891 (mt0) REVERT: C 222 LEU cc_start: 0.8062 (tp) cc_final: 0.7822 (tp) REVERT: C 225 CYS cc_start: 0.8599 (m) cc_final: 0.8359 (m) REVERT: C 236 LYS cc_start: 0.8828 (mppt) cc_final: 0.8291 (mppt) REVERT: C 264 VAL cc_start: 0.7933 (m) cc_final: 0.7636 (p) REVERT: C 267 ARG cc_start: 0.8025 (ppt170) cc_final: 0.7400 (ppt170) REVERT: C 268 GLU cc_start: 0.8325 (pp20) cc_final: 0.6780 (tm-30) REVERT: C 306 MET cc_start: 0.8178 (tmm) cc_final: 0.7484 (tmm) REVERT: C 308 ARG cc_start: 0.8421 (ttp-170) cc_final: 0.8199 (ttp-170) REVERT: C 316 MET cc_start: 0.7475 (mtt) cc_final: 0.7272 (mtt) REVERT: C 323 GLN cc_start: 0.8795 (mt0) cc_final: 0.8494 (mm110) REVERT: C 351 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8750 (tttm) REVERT: C 357 GLN cc_start: 0.8150 (tt0) cc_final: 0.7316 (tt0) REVERT: C 369 ARG cc_start: 0.8459 (mmp-170) cc_final: 0.8259 (mmp-170) REVERT: C 410 GLU cc_start: 0.8373 (tt0) cc_final: 0.8015 (tt0) REVERT: C 411 TYR cc_start: 0.8670 (t80) cc_final: 0.8458 (t80) REVERT: C 454 GLU cc_start: 0.8185 (pt0) cc_final: 0.7918 (pt0) REVERT: C 464 GLU cc_start: 0.6972 (mp0) cc_final: 0.6748 (mp0) REVERT: C 494 LEU cc_start: 0.8197 (tp) cc_final: 0.7895 (tt) REVERT: C 504 GLU cc_start: 0.8487 (tp30) cc_final: 0.8077 (tp30) REVERT: C 520 ASN cc_start: 0.8384 (m110) cc_final: 0.7936 (m110) REVERT: C 536 LYS cc_start: 0.7943 (ttmt) cc_final: 0.7521 (ttmt) REVERT: C 549 TYR cc_start: 0.7727 (m-80) cc_final: 0.7351 (m-80) REVERT: C 550 LYS cc_start: 0.8421 (mttt) cc_final: 0.8218 (mttt) REVERT: C 566 LYS cc_start: 0.8790 (pttp) cc_final: 0.8426 (pttp) REVERT: C 582 LEU cc_start: 0.8945 (mt) cc_final: 0.8713 (mt) REVERT: C 584 HIS cc_start: 0.8535 (m90) cc_final: 0.8293 (m90) REVERT: C 603 MET cc_start: 0.7701 (mtt) cc_final: 0.7464 (mtt) REVERT: C 606 LEU cc_start: 0.8750 (mp) cc_final: 0.8545 (mp) REVERT: D 18 ASP cc_start: 0.6314 (m-30) cc_final: 0.5990 (m-30) REVERT: D 32 ASN cc_start: 0.9122 (t0) cc_final: 0.8914 (t0) REVERT: D 78 ASN cc_start: 0.9160 (t0) cc_final: 0.8541 (t0) REVERT: D 87 GLU cc_start: 0.8169 (tp30) cc_final: 0.7894 (mm-30) REVERT: D 89 GLN cc_start: 0.8925 (mm110) cc_final: 0.8652 (mm110) REVERT: D 103 HIS cc_start: 0.6749 (m-70) cc_final: 0.6528 (m-70) REVERT: D 109 VAL cc_start: 0.7974 (p) cc_final: 0.7652 (p) REVERT: D 142 LEU cc_start: 0.8040 (mt) cc_final: 0.7771 (mt) REVERT: D 157 LEU cc_start: 0.8708 (mm) cc_final: 0.8263 (mm) REVERT: D 158 ILE cc_start: 0.9069 (tt) cc_final: 0.8782 (pt) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2708 time to fit residues: 173.3339 Evaluate side-chains 425 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 2.9990 chunk 134 optimal weight: 0.0970 chunk 126 optimal weight: 0.0970 chunk 2 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 53 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 131 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 overall best weight: 0.3574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 GLN C 248 ASN C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS D 42 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.155910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120767 restraints weight = 30108.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.125170 restraints weight = 17486.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128199 restraints weight = 11489.196| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14205 Z= 0.148 Angle : 0.778 13.550 19562 Z= 0.403 Chirality : 0.045 0.235 2195 Planarity : 0.005 0.068 2244 Dihedral : 21.224 168.282 2554 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.21), residues: 1535 helix: -0.07 (0.21), residues: 592 sheet: -0.58 (0.35), residues: 238 loop : -1.73 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 406 HIS 0.014 0.001 HIS A 229 PHE 0.046 0.002 PHE A 589 TYR 0.028 0.002 TYR A 41 ARG 0.012 0.001 ARG C 591 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 580) hydrogen bonds : angle 5.24654 ( 1605) covalent geometry : bond 0.00324 (14204) covalent geometry : angle 0.77788 (19562) Misc. bond : bond 0.00093 ( 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 467 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 467 time to evaluate : 1.395 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: 0.6260 (tmm) cc_final: 0.6051 (tmm) REVERT: A 65 ASP cc_start: 0.8601 (t70) cc_final: 0.8238 (t0) REVERT: A 66 PHE cc_start: 0.7249 (m-80) cc_final: 0.6876 (m-80) REVERT: A 90 LYS cc_start: 0.7891 (pptt) cc_final: 0.7197 (ptmm) REVERT: A 181 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8310 (ttp80) REVERT: A 224 PHE cc_start: 0.8038 (m-10) cc_final: 0.7781 (m-10) REVERT: A 231 LYS cc_start: 0.9074 (mptt) cc_final: 0.8754 (mptt) REVERT: A 232 ILE cc_start: 0.8767 (mt) cc_final: 0.8551 (mt) REVERT: A 255 LEU cc_start: 0.7861 (mt) cc_final: 0.7607 (mt) REVERT: A 260 ASP cc_start: 0.7971 (p0) cc_final: 0.7768 (p0) REVERT: A 272 MET cc_start: 0.7485 (mtt) cc_final: 0.7197 (mtt) REVERT: A 293 LYS cc_start: 0.7996 (pttm) cc_final: 0.7564 (pttm) REVERT: A 297 ARG cc_start: 0.6314 (ptm160) cc_final: 0.5807 (ptm160) REVERT: A 303 THR cc_start: 0.8461 (m) cc_final: 0.8161 (p) REVERT: A 305 GLU cc_start: 0.8671 (tt0) cc_final: 0.7837 (tp30) REVERT: A 346 GLU cc_start: 0.7781 (mp0) cc_final: 0.7528 (mp0) REVERT: A 348 PHE cc_start: 0.8935 (t80) cc_final: 0.8536 (t80) REVERT: A 351 LYS cc_start: 0.8649 (mttm) cc_final: 0.7598 (mmtm) REVERT: A 355 ARG cc_start: 0.8410 (ttm110) cc_final: 0.7594 (ttm110) REVERT: A 368 LYS cc_start: 0.8802 (mtpt) cc_final: 0.8483 (mtpt) REVERT: A 369 ARG cc_start: 0.9162 (ptm-80) cc_final: 0.8756 (ptm-80) REVERT: A 370 LEU cc_start: 0.9014 (tt) cc_final: 0.8551 (tt) REVERT: A 380 LYS cc_start: 0.8437 (ttpt) cc_final: 0.8082 (ttmt) REVERT: A 382 HIS cc_start: 0.7621 (t-90) cc_final: 0.7157 (t-90) REVERT: A 398 GLU cc_start: 0.7338 (pm20) cc_final: 0.7079 (pm20) REVERT: A 409 TYR cc_start: 0.8666 (t80) cc_final: 0.8264 (t80) REVERT: A 482 LYS cc_start: 0.7741 (mmmm) cc_final: 0.7078 (mmmm) REVERT: A 502 LEU cc_start: 0.9053 (pp) cc_final: 0.8625 (pp) REVERT: A 516 VAL cc_start: 0.8824 (m) cc_final: 0.8320 (p) REVERT: A 518 ILE cc_start: 0.8898 (mm) cc_final: 0.8653 (tp) REVERT: A 520 ASN cc_start: 0.8824 (m-40) cc_final: 0.8436 (m-40) REVERT: A 525 ASN cc_start: 0.7186 (m-40) cc_final: 0.6573 (m110) REVERT: A 560 ILE cc_start: 0.8206 (mt) cc_final: 0.7879 (pt) REVERT: A 565 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7563 (mt-10) REVERT: A 569 ASN cc_start: 0.7165 (m110) cc_final: 0.6860 (m110) REVERT: B 106 CYS cc_start: 0.7930 (t) cc_final: 0.7565 (p) REVERT: B 128 LYS cc_start: 0.8437 (tttm) cc_final: 0.7988 (tttm) REVERT: C 15 GLN cc_start: 0.8535 (pp30) cc_final: 0.8258 (pp30) REVERT: C 30 LYS cc_start: 0.8194 (mttt) cc_final: 0.7947 (mttt) REVERT: C 32 LEU cc_start: 0.7963 (mt) cc_final: 0.7628 (mt) REVERT: C 41 TYR cc_start: 0.7156 (p90) cc_final: 0.6937 (p90) REVERT: C 53 LYS cc_start: 0.6616 (mppt) cc_final: 0.5997 (mppt) REVERT: C 71 ASN cc_start: 0.7626 (m110) cc_final: 0.7356 (m110) REVERT: C 95 LYS cc_start: 0.9098 (mppt) cc_final: 0.8647 (mppt) REVERT: C 98 MET cc_start: 0.7422 (ttt) cc_final: 0.6897 (ttt) REVERT: C 125 ILE cc_start: 0.7604 (mm) cc_final: 0.7353 (mm) REVERT: C 128 GLU cc_start: 0.7704 (mt-10) cc_final: 0.6952 (mt-10) REVERT: C 139 LYS cc_start: 0.7732 (tmmt) cc_final: 0.7118 (pttp) REVERT: C 144 GLU cc_start: 0.7227 (tp30) cc_final: 0.6773 (tm-30) REVERT: C 159 ASP cc_start: 0.7572 (t0) cc_final: 0.6890 (t0) REVERT: C 164 MET cc_start: 0.8611 (ppp) cc_final: 0.8323 (ppp) REVERT: C 199 TYR cc_start: 0.8048 (t80) cc_final: 0.7627 (t80) REVERT: C 204 TYR cc_start: 0.7802 (m-80) cc_final: 0.7398 (m-10) REVERT: C 218 GLN cc_start: 0.7436 (mt0) cc_final: 0.6942 (mt0) REVERT: C 225 CYS cc_start: 0.8531 (m) cc_final: 0.8277 (m) REVERT: C 236 LYS cc_start: 0.8765 (mppt) cc_final: 0.8240 (mppt) REVERT: C 267 ARG cc_start: 0.8008 (ppt170) cc_final: 0.7449 (ppt170) REVERT: C 306 MET cc_start: 0.8130 (tmm) cc_final: 0.7569 (tmm) REVERT: C 323 GLN cc_start: 0.8748 (mt0) cc_final: 0.8441 (mm110) REVERT: C 351 LYS cc_start: 0.9054 (ttmm) cc_final: 0.8717 (tttm) REVERT: C 357 GLN cc_start: 0.8036 (tt0) cc_final: 0.7489 (tt0) REVERT: C 367 VAL cc_start: 0.8990 (t) cc_final: 0.8648 (p) REVERT: C 410 GLU cc_start: 0.8320 (tt0) cc_final: 0.7955 (tt0) REVERT: C 415 HIS cc_start: 0.7798 (t-170) cc_final: 0.7501 (t-170) REVERT: C 454 GLU cc_start: 0.8128 (pt0) cc_final: 0.7911 (pt0) REVERT: C 464 GLU cc_start: 0.6980 (mp0) cc_final: 0.6724 (mp0) REVERT: C 494 LEU cc_start: 0.8208 (tp) cc_final: 0.7897 (tt) REVERT: C 504 GLU cc_start: 0.8414 (tp30) cc_final: 0.7983 (tp30) REVERT: C 520 ASN cc_start: 0.8277 (m110) cc_final: 0.7863 (m110) REVERT: C 536 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7450 (ttmt) REVERT: C 566 LYS cc_start: 0.8760 (pttp) cc_final: 0.8306 (pttp) REVERT: C 582 LEU cc_start: 0.8937 (mt) cc_final: 0.8731 (mt) REVERT: C 584 HIS cc_start: 0.8501 (m90) cc_final: 0.8265 (m90) REVERT: C 591 ARG cc_start: 0.8239 (mmm160) cc_final: 0.7675 (mmm160) REVERT: C 603 MET cc_start: 0.7562 (mtt) cc_final: 0.7352 (mtt) REVERT: C 606 LEU cc_start: 0.8747 (mp) cc_final: 0.8524 (mp) REVERT: D 32 ASN cc_start: 0.9061 (t0) cc_final: 0.8834 (t0) REVERT: D 78 ASN cc_start: 0.9005 (t0) cc_final: 0.8279 (t0) REVERT: D 87 GLU cc_start: 0.8138 (tp30) cc_final: 0.7860 (mm-30) REVERT: D 89 GLN cc_start: 0.8919 (mm110) cc_final: 0.8690 (mm110) REVERT: D 103 HIS cc_start: 0.6776 (m-70) cc_final: 0.6558 (m-70) outliers start: 0 outliers final: 0 residues processed: 467 average time/residue: 0.2715 time to fit residues: 177.8757 Evaluate side-chains 425 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 157 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 103 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN C 39 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 519 ASN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.153547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118591 restraints weight = 30463.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.122947 restraints weight = 17724.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.125942 restraints weight = 11651.184| |-----------------------------------------------------------------------------| r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14205 Z= 0.172 Angle : 0.768 12.648 19562 Z= 0.402 Chirality : 0.045 0.203 2195 Planarity : 0.005 0.064 2244 Dihedral : 21.229 170.048 2554 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.06 % Favored : 90.88 % Rotamer: Outliers : 0.07 % Allowed : 0.30 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.21), residues: 1535 helix: -0.07 (0.21), residues: 593 sheet: -0.60 (0.36), residues: 220 loop : -1.79 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.003 TRP C 259 HIS 0.011 0.001 HIS A 229 PHE 0.036 0.002 PHE A 589 TYR 0.021 0.002 TYR C 578 ARG 0.017 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04462 ( 580) hydrogen bonds : angle 5.28695 ( 1605) covalent geometry : bond 0.00368 (14204) covalent geometry : angle 0.76776 (19562) Misc. bond : bond 0.00108 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5244.86 seconds wall clock time: 92 minutes 9.90 seconds (5529.90 seconds total)