Starting phenix.real_space_refine on Thu Sep 18 03:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9w_45374/09_2025/9c9w_45374_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9w_45374/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9c9w_45374/09_2025/9c9w_45374_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9w_45374/09_2025/9c9w_45374_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c9w_45374/09_2025/9c9w_45374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9w_45374/09_2025/9c9w_45374.map" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 80 5.49 5 S 78 5.16 5 C 8443 2.51 5 N 2385 2.21 5 O 2774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13761 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4841 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 475 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.07, per 1000 atoms: 0.22 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: 1.20 Conformation dependent library (CDL) restraints added in 628.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 42.4% alpha, 15.7% beta 25 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 1.61 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: 2.23 Time building geometry restraints manager: 1.58 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: 2.920 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: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- 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 : 19.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.58 % Favored : 90.23 % Rotamer: Outliers : 0.15 % Allowed : 1.12 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.21), residues: 1535 helix: -0.20 (0.21), residues: 581 sheet: -0.83 (0.35), residues: 224 loop : -1.75 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 308 TYR 0.026 0.002 TYR A 595 PHE 0.041 0.002 PHE A 589 TRP 0.023 0.002 TRP C 363 HIS 0.005 0.001 HIS C 39 Details of bonding type rmsd covalent geometry : bond 0.00356 (14204) covalent geometry : angle 0.80187 (19562) hydrogen bonds : bond 0.16309 ( 580) hydrogen bonds : angle 6.96821 ( 1605) 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 : 0.501 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: 0.1492 time to fit residues: 95.9547 Evaluate side-chains 410 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 A 519 ASN A 523 GLN ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 573 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.152960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119001 restraints weight = 30192.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.123246 restraints weight = 17382.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.126094 restraints weight = 11348.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128184 restraints weight = 8103.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129494 restraints weight = 6176.579| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 14205 Z= 0.247 Angle : 0.741 9.755 19562 Z= 0.403 Chirality : 0.045 0.280 2195 Planarity : 0.005 0.050 2244 Dihedral : 21.166 169.451 2554 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.84 % Favored : 90.10 % Rotamer: Outliers : 0.52 % Allowed : 6.67 % Favored : 92.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.68 (0.21), residues: 1535 helix: -0.37 (0.20), residues: 588 sheet: -0.40 (0.37), residues: 222 loop : -1.97 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 308 TYR 0.023 0.002 TYR A 595 PHE 0.031 0.002 PHE A 589 TRP 0.034 0.003 TRP C 406 HIS 0.009 0.001 HIS A 387 Details of bonding type rmsd covalent geometry : bond 0.00501 (14204) covalent geometry : angle 0.74125 (19562) hydrogen bonds : bond 0.05356 ( 580) hydrogen bonds : angle 5.72576 ( 1605) Misc. bond : bond 0.00188 ( 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 462 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 455 time to evaluate : 0.521 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 1 MET cc_start: 0.7707 (tpt) cc_final: 0.7326 (tpt) REVERT: A 2 LYS cc_start: 0.9159 (mttt) cc_final: 0.8330 (mttp) REVERT: A 51 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8334 (mtm-85) REVERT: A 66 PHE cc_start: 0.7223 (m-80) cc_final: 0.7000 (m-80) REVERT: A 119 ASP cc_start: 0.8657 (p0) cc_final: 0.8430 (p0) REVERT: A 178 VAL cc_start: 0.8679 (p) cc_final: 0.8371 (p) REVERT: A 181 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8167 (ttp80) REVERT: A 222 LEU cc_start: 0.8793 (tp) cc_final: 0.8505 (tp) REVERT: A 231 LYS cc_start: 0.8990 (mptt) cc_final: 0.8711 (mptt) REVERT: A 255 LEU cc_start: 0.7881 (mt) cc_final: 0.7484 (mm) REVERT: A 260 ASP cc_start: 0.7762 (p0) cc_final: 0.7496 (p0) REVERT: A 293 LYS cc_start: 0.8031 (pttm) cc_final: 0.7380 (pttm) REVERT: A 297 ARG cc_start: 0.6148 (ptm160) cc_final: 0.5843 (ptm160) REVERT: A 322 MET cc_start: 0.8716 (mmm) cc_final: 0.8290 (mmm) REVERT: A 326 GLU cc_start: 0.8410 (mt-10) cc_final: 0.7974 (mt-10) REVERT: A 346 GLU cc_start: 0.7689 (mp0) cc_final: 0.7369 (mp0) REVERT: A 351 LYS cc_start: 0.8643 (tttp) cc_final: 0.7503 (mmtm) REVERT: A 360 HIS cc_start: 0.8063 (t-90) cc_final: 0.7614 (t-90) REVERT: A 368 LYS cc_start: 0.8837 (mtpt) cc_final: 0.8511 (mtpt) REVERT: A 379 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7436 (mtp85) REVERT: A 382 HIS cc_start: 0.7453 (t-90) cc_final: 0.7147 (t-90) REVERT: A 406 TRP cc_start: 0.8906 (t60) cc_final: 0.8570 (t60) REVERT: A 409 TYR cc_start: 0.8635 (t80) cc_final: 0.8263 (t80) REVERT: A 426 TYR cc_start: 0.7187 (p90) cc_final: 0.6785 (p90) REVERT: A 456 MET cc_start: 0.8198 (mtm) cc_final: 0.7989 (mtm) REVERT: A 489 ASN cc_start: 0.7346 (p0) cc_final: 0.6945 (p0) REVERT: A 498 GLU cc_start: 0.8297 (mp0) cc_final: 0.8061 (mp0) REVERT: A 505 LYS cc_start: 0.9298 (tmtt) cc_final: 0.8908 (tmtt) REVERT: A 516 VAL cc_start: 0.8917 (m) cc_final: 0.8320 (p) REVERT: A 519 ASN cc_start: 0.7812 (m110) cc_final: 0.7607 (m110) REVERT: A 520 ASN cc_start: 0.8775 (m-40) cc_final: 0.8444 (m-40) REVERT: A 525 ASN cc_start: 0.7069 (m-40) cc_final: 0.6538 (m110) REVERT: A 526 TYR cc_start: 0.6982 (m-10) cc_final: 0.6261 (m-80) REVERT: A 530 GLU cc_start: 0.5220 (mp0) cc_final: 0.4538 (mp0) REVERT: A 544 LEU cc_start: 0.8890 (tp) cc_final: 0.8510 (tp) REVERT: A 565 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7724 (mt-10) REVERT: A 603 MET cc_start: 0.8472 (mtm) cc_final: 0.8264 (mtm) REVERT: B 1 MET cc_start: 0.6528 (ptt) cc_final: 0.6308 (ptt) REVERT: C 6 MET cc_start: 0.7457 (ptm) cc_final: 0.7240 (ptm) REVERT: C 30 LYS cc_start: 0.8027 (mttt) cc_final: 0.7819 (mttt) REVERT: C 32 LEU cc_start: 0.7981 (mt) cc_final: 0.7775 (mt) REVERT: C 53 LYS cc_start: 0.7721 (mppt) cc_final: 0.6850 (mppt) REVERT: C 66 PHE cc_start: 0.7306 (m-80) cc_final: 0.7053 (m-80) REVERT: C 95 LYS cc_start: 0.9112 (mppt) cc_final: 0.8641 (mppt) REVERT: C 125 ILE cc_start: 0.7572 (mm) cc_final: 0.7279 (mm) REVERT: C 128 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7016 (mt-10) REVERT: C 139 LYS cc_start: 0.7347 (tmmt) cc_final: 0.6904 (tttm) REVERT: C 144 GLU cc_start: 0.7140 (tp30) cc_final: 0.6828 (tp30) REVERT: C 204 TYR cc_start: 0.7727 (m-80) cc_final: 0.7365 (m-10) REVERT: C 232 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7885 (mp) REVERT: C 236 LYS cc_start: 0.8737 (mppt) cc_final: 0.8134 (mppt) REVERT: C 244 GLN cc_start: 0.6196 (tp-100) cc_final: 0.5964 (tp40) REVERT: C 262 VAL cc_start: 0.8900 (m) cc_final: 0.8689 (p) REVERT: C 302 ASN cc_start: 0.8187 (t0) cc_final: 0.7909 (m-40) REVERT: C 306 MET cc_start: 0.8010 (tmm) cc_final: 0.7335 (tmm) REVERT: C 308 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.8429 (ttm-80) REVERT: C 323 GLN cc_start: 0.8780 (mt0) cc_final: 0.8423 (mm110) REVERT: C 351 LYS cc_start: 0.8972 (ttmm) cc_final: 0.8232 (tttm) REVERT: C 365 ASP cc_start: 0.8129 (p0) cc_final: 0.7783 (p0) REVERT: C 368 LYS cc_start: 0.9136 (ttmm) cc_final: 0.8817 (ttmm) REVERT: C 398 GLU cc_start: 0.8022 (tt0) cc_final: 0.7151 (tt0) REVERT: C 410 GLU cc_start: 0.8323 (tt0) cc_final: 0.7979 (tt0) REVERT: C 438 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7138 (mm-30) REVERT: C 442 CYS cc_start: 0.6791 (p) cc_final: 0.6476 (m) REVERT: C 476 PHE cc_start: 0.7927 (m-80) cc_final: 0.7600 (m-80) REVERT: C 503 MET cc_start: 0.8463 (tpp) cc_final: 0.8046 (tpp) REVERT: C 504 GLU cc_start: 0.8631 (tp30) cc_final: 0.8248 (tp30) REVERT: C 523 GLN cc_start: 0.8408 (tt0) cc_final: 0.7731 (tp-100) REVERT: C 550 LYS cc_start: 0.8347 (mttt) cc_final: 0.8082 (mttt) REVERT: C 557 LEU cc_start: 0.8947 (mm) cc_final: 0.8620 (mm) REVERT: C 566 LYS cc_start: 0.8722 (pttp) cc_final: 0.8345 (pttp) REVERT: C 584 HIS cc_start: 0.8504 (m90) cc_final: 0.8167 (m90) REVERT: C 590 LYS cc_start: 0.8559 (tttt) cc_final: 0.8223 (tttt) REVERT: C 606 LEU cc_start: 0.8742 (mp) cc_final: 0.8502 (mp) REVERT: D 18 ASP cc_start: 0.6269 (m-30) cc_final: 0.5961 (m-30) REVERT: D 78 ASN cc_start: 0.9129 (t0) cc_final: 0.8732 (t0) REVERT: D 87 GLU cc_start: 0.8205 (tp30) cc_final: 0.7712 (mm-30) REVERT: D 99 MET cc_start: 0.6954 (ttm) cc_final: 0.6276 (ttm) REVERT: D 140 LEU cc_start: 0.8999 (tt) cc_final: 0.8737 (tt) outliers start: 7 outliers final: 1 residues processed: 457 average time/residue: 0.1391 time to fit residues: 88.3778 Evaluate side-chains 416 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 414 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 156 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN B 146 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 218 GLN C 356 GLN C 415 HIS D 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.154195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.120153 restraints weight = 30177.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.124432 restraints weight = 17247.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.127325 restraints weight = 11203.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.129267 restraints weight = 7967.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130802 restraints weight = 6123.118| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14205 Z= 0.181 Angle : 0.705 10.706 19562 Z= 0.374 Chirality : 0.043 0.166 2195 Planarity : 0.005 0.052 2244 Dihedral : 21.199 168.322 2554 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.93 % Favored : 91.01 % Rotamer: Outliers : 0.30 % Allowed : 5.62 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.21), residues: 1535 helix: -0.16 (0.21), residues: 588 sheet: -0.39 (0.37), residues: 215 loop : -1.89 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 46 TYR 0.023 0.002 TYR C 411 PHE 0.046 0.002 PHE A 589 TRP 0.013 0.001 TRP C 259 HIS 0.007 0.001 HIS C 60 Details of bonding type rmsd covalent geometry : bond 0.00375 (14204) covalent geometry : angle 0.70467 (19562) hydrogen bonds : bond 0.04849 ( 580) hydrogen bonds : angle 5.47185 ( 1605) Misc. bond : bond 0.00128 ( 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 470 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 466 time to evaluate : 0.489 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: 0.9121 (mttt) cc_final: 0.8822 (mttp) REVERT: A 62 MET cc_start: 0.6023 (tmm) cc_final: 0.5822 (tmm) REVERT: A 65 ASP cc_start: 0.8601 (t70) cc_final: 0.8300 (t0) REVERT: A 66 PHE cc_start: 0.7203 (m-80) cc_final: 0.6977 (m-80) REVERT: A 119 ASP cc_start: 0.8715 (p0) cc_final: 0.8484 (p0) REVERT: A 226 VAL cc_start: 0.8762 (p) cc_final: 0.8524 (p) REVERT: A 231 LYS cc_start: 0.8996 (mptt) cc_final: 0.8746 (mptt) REVERT: A 236 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8691 (tppt) REVERT: A 246 LYS cc_start: 0.7358 (tmtt) cc_final: 0.6977 (tmtt) REVERT: A 255 LEU cc_start: 0.7796 (mt) cc_final: 0.7262 (mm) REVERT: A 260 ASP cc_start: 0.7811 (p0) cc_final: 0.7578 (p0) REVERT: A 290 ARG cc_start: 0.8414 (ppt170) cc_final: 0.7849 (ppt170) REVERT: A 293 LYS cc_start: 0.7968 (pttm) cc_final: 0.7272 (pttm) REVERT: A 297 ARG cc_start: 0.6004 (ptm160) cc_final: 0.5804 (ptm160) REVERT: A 305 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8214 (tp30) REVERT: A 316 MET cc_start: 0.7301 (tmm) cc_final: 0.6825 (tmm) REVERT: A 320 HIS cc_start: 0.7096 (t-90) cc_final: 0.6746 (t-90) REVERT: A 346 GLU cc_start: 0.7772 (mp0) cc_final: 0.7429 (mp0) REVERT: A 351 LYS cc_start: 0.8252 (tttp) cc_final: 0.7738 (tppt) REVERT: A 355 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7731 (ttm110) REVERT: A 360 HIS cc_start: 0.8138 (t-90) cc_final: 0.7591 (t-90) REVERT: A 366 THR cc_start: 0.8674 (p) cc_final: 0.8473 (p) REVERT: A 368 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8491 (mtpt) REVERT: A 369 ARG cc_start: 0.9078 (ptm-80) cc_final: 0.8701 (ptm-80) REVERT: A 370 LEU cc_start: 0.8931 (tt) cc_final: 0.8465 (tt) REVERT: A 379 ARG cc_start: 0.7740 (mtp85) cc_final: 0.7402 (mtp85) REVERT: A 382 HIS cc_start: 0.7414 (t-90) cc_final: 0.7109 (t-90) REVERT: A 394 LYS cc_start: 0.8684 (ttpt) cc_final: 0.8480 (ttpt) REVERT: A 406 TRP cc_start: 0.8861 (t60) cc_final: 0.8560 (t60) REVERT: A 409 TYR cc_start: 0.8658 (t80) cc_final: 0.8221 (t80) REVERT: A 426 TYR cc_start: 0.7219 (p90) cc_final: 0.6774 (p90) REVERT: A 472 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7382 (ttp80) REVERT: A 482 LYS cc_start: 0.7712 (mmmm) cc_final: 0.6903 (mmmm) REVERT: A 489 ASN cc_start: 0.7313 (p0) cc_final: 0.6949 (p0) REVERT: A 505 LYS cc_start: 0.9293 (tmtt) cc_final: 0.8878 (tmtt) REVERT: A 516 VAL cc_start: 0.8875 (m) cc_final: 0.8244 (p) REVERT: A 519 ASN cc_start: 0.7826 (m110) cc_final: 0.7571 (m110) REVERT: A 520 ASN cc_start: 0.8809 (m-40) cc_final: 0.8481 (m-40) REVERT: A 530 GLU cc_start: 0.5240 (mp0) cc_final: 0.4727 (mp0) REVERT: A 565 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7576 (mt-10) REVERT: A 569 ASN cc_start: 0.7171 (m110) cc_final: 0.6882 (m110) REVERT: A 603 MET cc_start: 0.8444 (mtm) cc_final: 0.8243 (mtm) REVERT: B 1 MET cc_start: 0.6399 (ptt) cc_final: 0.6189 (ptt) REVERT: B 136 LYS cc_start: 0.7695 (mmpt) cc_final: 0.7045 (mmpt) REVERT: B 154 VAL cc_start: 0.8391 (p) cc_final: 0.8003 (p) REVERT: C 6 MET cc_start: 0.7429 (ptm) cc_final: 0.7223 (ptm) REVERT: C 15 GLN cc_start: 0.8413 (pp30) cc_final: 0.8090 (pp30) REVERT: C 30 LYS cc_start: 0.8029 (mttt) cc_final: 0.7814 (mttt) REVERT: C 32 LEU cc_start: 0.7897 (mt) cc_final: 0.7670 (mt) REVERT: C 41 TYR cc_start: 0.7175 (p90) cc_final: 0.6925 (p90) REVERT: C 53 LYS cc_start: 0.7519 (mppt) cc_final: 0.6671 (mppt) REVERT: C 95 LYS cc_start: 0.9131 (mppt) cc_final: 0.8686 (mppt) REVERT: C 98 MET cc_start: 0.7439 (ttm) cc_final: 0.7212 (ttm) REVERT: C 128 GLU cc_start: 0.7545 (mt-10) cc_final: 0.6946 (mt-10) REVERT: C 139 LYS cc_start: 0.7589 (tmmt) cc_final: 0.7114 (ptmm) REVERT: C 144 GLU cc_start: 0.7082 (tp30) cc_final: 0.6769 (tp30) REVERT: C 152 PHE cc_start: 0.7833 (p90) cc_final: 0.7607 (p90) REVERT: C 159 ASP cc_start: 0.7547 (t0) cc_final: 0.7248 (t0) REVERT: C 164 MET cc_start: 0.8644 (ppp) cc_final: 0.8421 (ppp) REVERT: C 204 TYR cc_start: 0.7679 (m-80) cc_final: 0.7439 (m-10) REVERT: C 232 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7915 (mp) REVERT: C 236 LYS cc_start: 0.8722 (mppt) cc_final: 0.8136 (mppt) REVERT: C 244 GLN cc_start: 0.6037 (tp-100) cc_final: 0.5766 (tp40) REVERT: C 267 ARG cc_start: 0.8032 (ppt170) cc_final: 0.7611 (ppt170) REVERT: C 302 ASN cc_start: 0.8322 (t0) cc_final: 0.7914 (m-40) REVERT: C 306 MET cc_start: 0.8042 (tmm) cc_final: 0.7343 (tmm) REVERT: C 323 GLN cc_start: 0.8776 (mt0) cc_final: 0.8443 (mm110) REVERT: C 351 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8784 (tttm) REVERT: C 365 ASP cc_start: 0.7998 (p0) cc_final: 0.7672 (p0) REVERT: C 410 GLU cc_start: 0.8308 (tt0) cc_final: 0.7976 (tt0) REVERT: C 438 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7246 (tp30) REVERT: C 442 CYS cc_start: 0.6771 (p) cc_final: 0.6472 (m) REVERT: C 449 SER cc_start: 0.8625 (t) cc_final: 0.8418 (t) REVERT: C 454 GLU cc_start: 0.7949 (pt0) cc_final: 0.7698 (pt0) REVERT: C 476 PHE cc_start: 0.7982 (m-80) cc_final: 0.7688 (m-80) REVERT: C 499 LEU cc_start: 0.8624 (tp) cc_final: 0.8416 (tt) REVERT: C 503 MET cc_start: 0.8379 (tpp) cc_final: 0.8021 (tpp) REVERT: C 504 GLU cc_start: 0.8614 (tp30) cc_final: 0.8173 (tp30) REVERT: C 550 LYS cc_start: 0.8340 (mttt) cc_final: 0.8083 (mttt) REVERT: C 557 LEU cc_start: 0.8976 (mm) cc_final: 0.8594 (mm) REVERT: C 566 LYS cc_start: 0.8734 (pttp) cc_final: 0.8360 (pttp) REVERT: C 582 LEU cc_start: 0.8963 (mt) cc_final: 0.8487 (mt) REVERT: C 584 HIS cc_start: 0.8517 (m90) cc_final: 0.8183 (m90) REVERT: C 590 LYS cc_start: 0.8560 (tttt) cc_final: 0.8195 (tttt) REVERT: C 603 MET cc_start: 0.7650 (mtt) cc_final: 0.7404 (mtt) REVERT: C 606 LEU cc_start: 0.8729 (mp) cc_final: 0.8484 (mp) REVERT: D 18 ASP cc_start: 0.6341 (m-30) cc_final: 0.5923 (m-30) REVERT: D 78 ASN cc_start: 0.9121 (t0) cc_final: 0.8663 (t0) REVERT: D 87 GLU cc_start: 0.8054 (tp30) cc_final: 0.7817 (mm-30) REVERT: D 140 LEU cc_start: 0.8984 (tt) cc_final: 0.8769 (tt) REVERT: D 157 LEU cc_start: 0.8701 (mm) cc_final: 0.8325 (mm) outliers start: 4 outliers final: 1 residues processed: 467 average time/residue: 0.1292 time to fit residues: 84.5650 Evaluate side-chains 426 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 424 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 103 optimal weight: 0.0970 chunk 157 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 356 GLN C 360 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.155307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120707 restraints weight = 29887.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125120 restraints weight = 17169.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128074 restraints weight = 11178.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.130170 restraints weight = 7961.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.131626 restraints weight = 6087.048| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14205 Z= 0.149 Angle : 0.675 10.091 19562 Z= 0.358 Chirality : 0.042 0.176 2195 Planarity : 0.005 0.067 2244 Dihedral : 21.182 167.787 2554 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 0.22 % Allowed : 4.04 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.21), residues: 1535 helix: -0.05 (0.21), residues: 584 sheet: -0.55 (0.36), residues: 233 loop : -1.75 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 308 TYR 0.026 0.002 TYR A 41 PHE 0.031 0.002 PHE A 589 TRP 0.017 0.002 TRP A 241 HIS 0.011 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00319 (14204) covalent geometry : angle 0.67543 (19562) hydrogen bonds : bond 0.04469 ( 580) hydrogen bonds : angle 5.27021 ( 1605) Misc. bond : bond 0.00105 ( 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 460 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 457 time to evaluate : 0.543 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: 0.9114 (mttt) cc_final: 0.8823 (mttp) REVERT: A 65 ASP cc_start: 0.8577 (t70) cc_final: 0.8222 (t0) REVERT: A 66 PHE cc_start: 0.7264 (m-80) cc_final: 0.7003 (m-80) REVERT: A 181 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8282 (ttp80) REVERT: A 226 VAL cc_start: 0.8784 (p) cc_final: 0.8420 (p) REVERT: A 231 LYS cc_start: 0.8986 (mptt) cc_final: 0.8735 (mptt) REVERT: A 246 LYS cc_start: 0.7248 (tmtt) cc_final: 0.6880 (tmtt) REVERT: A 255 LEU cc_start: 0.7779 (mt) cc_final: 0.7272 (mm) REVERT: A 260 ASP cc_start: 0.7835 (p0) cc_final: 0.7617 (p0) REVERT: A 275 ASN cc_start: 0.8578 (m110) cc_final: 0.8196 (m110) REVERT: A 290 ARG cc_start: 0.8402 (ppt170) cc_final: 0.7827 (ppt170) REVERT: A 293 LYS cc_start: 0.7994 (pttm) cc_final: 0.7320 (pttm) REVERT: A 297 ARG cc_start: 0.6087 (ptm160) cc_final: 0.5868 (ptm160) REVERT: A 305 GLU cc_start: 0.8658 (mt-10) cc_final: 0.8196 (tp30) REVERT: A 346 GLU cc_start: 0.7799 (mp0) cc_final: 0.7459 (mp0) REVERT: A 348 PHE cc_start: 0.8767 (t80) cc_final: 0.8507 (t80) REVERT: A 351 LYS cc_start: 0.8255 (tttp) cc_final: 0.7519 (ttmm) REVERT: A 355 ARG cc_start: 0.8268 (ttm110) cc_final: 0.7633 (ttm110) REVERT: A 366 THR cc_start: 0.8630 (p) cc_final: 0.8405 (p) REVERT: A 368 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8481 (mtpt) REVERT: A 369 ARG cc_start: 0.9101 (ptm-80) cc_final: 0.8684 (ptm-80) REVERT: A 370 LEU cc_start: 0.8946 (tt) cc_final: 0.8455 (tt) REVERT: A 379 ARG cc_start: 0.7741 (mtp85) cc_final: 0.7371 (mtp85) REVERT: A 382 HIS cc_start: 0.7418 (t-90) cc_final: 0.7117 (t-90) REVERT: A 409 TYR cc_start: 0.8694 (t80) cc_final: 0.8306 (t80) REVERT: A 426 TYR cc_start: 0.7190 (p90) cc_final: 0.6775 (p90) REVERT: A 430 THR cc_start: 0.8214 (m) cc_final: 0.8012 (p) REVERT: A 489 ASN cc_start: 0.7275 (p0) cc_final: 0.6969 (p0) REVERT: A 505 LYS cc_start: 0.9259 (tmtt) cc_final: 0.8861 (tmtt) REVERT: A 516 VAL cc_start: 0.8834 (m) cc_final: 0.8215 (p) REVERT: A 518 ILE cc_start: 0.8874 (mm) cc_final: 0.8674 (tp) REVERT: A 519 ASN cc_start: 0.7813 (m110) cc_final: 0.7526 (m110) REVERT: A 520 ASN cc_start: 0.8797 (m-40) cc_final: 0.8450 (m-40) REVERT: A 560 ILE cc_start: 0.8278 (mt) cc_final: 0.8007 (pt) REVERT: A 565 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 569 ASN cc_start: 0.7059 (m110) cc_final: 0.6694 (m110) REVERT: A 603 MET cc_start: 0.8441 (mtm) cc_final: 0.8210 (mtm) REVERT: B 136 LYS cc_start: 0.7871 (mmpt) cc_final: 0.7109 (mmpt) REVERT: C 13 LEU cc_start: 0.8705 (tp) cc_final: 0.8303 (tp) REVERT: C 15 GLN cc_start: 0.8390 (pp30) cc_final: 0.8062 (pp30) REVERT: C 30 LYS cc_start: 0.8064 (mttt) cc_final: 0.7822 (mttt) REVERT: C 32 LEU cc_start: 0.7930 (mt) cc_final: 0.7699 (mt) REVERT: C 41 TYR cc_start: 0.7155 (p90) cc_final: 0.6895 (p90) REVERT: C 53 LYS cc_start: 0.7349 (mppt) cc_final: 0.6441 (mppt) REVERT: C 90 LYS cc_start: 0.8644 (ptmm) cc_final: 0.8130 (ptmm) REVERT: C 95 LYS cc_start: 0.9137 (mppt) cc_final: 0.8703 (mppt) REVERT: C 98 MET cc_start: 0.7449 (ttm) cc_final: 0.7242 (ttm) REVERT: C 128 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7039 (mt-10) REVERT: C 139 LYS cc_start: 0.7539 (tmmt) cc_final: 0.7111 (ptmm) REVERT: C 144 GLU cc_start: 0.7107 (tp30) cc_final: 0.6778 (tp30) REVERT: C 164 MET cc_start: 0.8602 (ppp) cc_final: 0.8349 (ppp) REVERT: C 204 TYR cc_start: 0.7685 (m-80) cc_final: 0.7435 (m-10) REVERT: C 218 GLN cc_start: 0.7426 (mt0) cc_final: 0.6992 (mt0) REVERT: C 232 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7855 (mp) REVERT: C 236 LYS cc_start: 0.8719 (mppt) cc_final: 0.8139 (mppt) REVERT: C 244 GLN cc_start: 0.6043 (tp-100) cc_final: 0.5753 (tp40) REVERT: C 263 ARG cc_start: 0.8333 (ptt180) cc_final: 0.6959 (ptt180) REVERT: C 267 ARG cc_start: 0.7993 (ppt170) cc_final: 0.7594 (ppt170) REVERT: C 292 GLU cc_start: 0.8660 (pm20) cc_final: 0.8340 (pm20) REVERT: C 302 ASN cc_start: 0.8340 (t0) cc_final: 0.7898 (m-40) REVERT: C 306 MET cc_start: 0.7992 (tmm) cc_final: 0.7310 (tmm) REVERT: C 308 ARG cc_start: 0.8804 (ttp-170) cc_final: 0.8578 (ttm-80) REVERT: C 323 GLN cc_start: 0.8754 (mt0) cc_final: 0.8434 (mm110) REVERT: C 351 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8734 (tttm) REVERT: C 357 GLN cc_start: 0.8117 (tt0) cc_final: 0.7823 (tt0) REVERT: C 365 ASP cc_start: 0.7921 (p0) cc_final: 0.7631 (p0) REVERT: C 410 GLU cc_start: 0.8331 (tt0) cc_final: 0.7960 (tt0) REVERT: C 430 THR cc_start: 0.7292 (t) cc_final: 0.7050 (t) REVERT: C 438 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7323 (tp30) REVERT: C 442 CYS cc_start: 0.6789 (p) cc_final: 0.6372 (m) REVERT: C 445 LYS cc_start: 0.8195 (mttm) cc_final: 0.7544 (mttm) REVERT: C 449 SER cc_start: 0.8624 (t) cc_final: 0.8423 (t) REVERT: C 476 PHE cc_start: 0.7946 (m-80) cc_final: 0.7633 (m-80) REVERT: C 504 GLU cc_start: 0.8590 (tp30) cc_final: 0.8191 (tp30) REVERT: C 550 LYS cc_start: 0.8348 (mttt) cc_final: 0.8096 (mttt) REVERT: C 557 LEU cc_start: 0.8957 (mm) cc_final: 0.8626 (mm) REVERT: C 566 LYS cc_start: 0.8706 (pttp) cc_final: 0.8325 (pttp) REVERT: C 582 LEU cc_start: 0.8899 (mt) cc_final: 0.8470 (mt) REVERT: C 584 HIS cc_start: 0.8500 (m90) cc_final: 0.8197 (m90) REVERT: C 590 LYS cc_start: 0.8548 (tttt) cc_final: 0.8189 (tttt) REVERT: C 603 MET cc_start: 0.7662 (mtt) cc_final: 0.7427 (mtt) REVERT: C 606 LEU cc_start: 0.8716 (mp) cc_final: 0.8477 (mp) REVERT: D 18 ASP cc_start: 0.6419 (m-30) cc_final: 0.6017 (m-30) REVERT: D 78 ASN cc_start: 0.9059 (t0) cc_final: 0.8288 (t0) REVERT: D 87 GLU cc_start: 0.8100 (tp30) cc_final: 0.7770 (mm-30) REVERT: D 103 HIS cc_start: 0.6557 (m-70) cc_final: 0.6295 (m90) REVERT: D 140 LEU cc_start: 0.8965 (tt) cc_final: 0.8748 (tt) outliers start: 3 outliers final: 0 residues processed: 457 average time/residue: 0.1290 time to fit residues: 82.5823 Evaluate side-chains 420 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 419 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 117 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 356 GLN C 357 GLN ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.155032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120556 restraints weight = 29888.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124863 restraints weight = 17172.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127861 restraints weight = 11284.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129955 restraints weight = 8013.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.131514 restraints weight = 6114.957| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14205 Z= 0.147 Angle : 0.685 11.527 19562 Z= 0.362 Chirality : 0.042 0.166 2195 Planarity : 0.005 0.054 2244 Dihedral : 21.177 168.202 2554 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.14 % Favored : 91.79 % Rotamer: Outliers : 0.22 % Allowed : 3.37 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.21), residues: 1535 helix: -0.04 (0.21), residues: 591 sheet: -0.45 (0.36), residues: 233 loop : -1.75 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 308 TYR 0.028 0.002 TYR A 41 PHE 0.068 0.002 PHE A 589 TRP 0.017 0.002 TRP A 115 HIS 0.008 0.001 HIS C 415 Details of bonding type rmsd covalent geometry : bond 0.00314 (14204) covalent geometry : angle 0.68465 (19562) hydrogen bonds : bond 0.04430 ( 580) hydrogen bonds : angle 5.20203 ( 1605) Misc. bond : bond 0.00092 ( 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 469 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 466 time to evaluate : 0.484 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: 0.9116 (mttt) cc_final: 0.8829 (mttp) REVERT: A 17 ILE cc_start: 0.9042 (mm) cc_final: 0.8746 (tp) REVERT: A 62 MET cc_start: 0.5866 (tmm) cc_final: 0.5633 (tmm) REVERT: A 65 ASP cc_start: 0.8607 (t70) cc_final: 0.8232 (t0) REVERT: A 66 PHE cc_start: 0.7173 (m-80) cc_final: 0.6898 (m-80) REVERT: A 119 ASP cc_start: 0.8823 (p0) cc_final: 0.8581 (p0) REVERT: A 181 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8195 (ttp80) REVERT: A 226 VAL cc_start: 0.8795 (p) cc_final: 0.8459 (p) REVERT: A 231 LYS cc_start: 0.9009 (mptt) cc_final: 0.8728 (mptt) REVERT: A 236 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8649 (tppt) REVERT: A 246 LYS cc_start: 0.7156 (tmtt) cc_final: 0.6820 (tmtt) REVERT: A 255 LEU cc_start: 0.7751 (mt) cc_final: 0.7337 (mt) REVERT: A 260 ASP cc_start: 0.7815 (p0) cc_final: 0.7491 (p0) REVERT: A 290 ARG cc_start: 0.8439 (ppt170) cc_final: 0.7860 (ppt170) REVERT: A 293 LYS cc_start: 0.7966 (pttm) cc_final: 0.7311 (pttm) REVERT: A 305 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8197 (tp30) REVERT: A 316 MET cc_start: 0.6763 (tmm) cc_final: 0.6266 (tmm) REVERT: A 320 HIS cc_start: 0.7126 (t-90) cc_final: 0.6744 (t-90) REVERT: A 324 THR cc_start: 0.8045 (p) cc_final: 0.7721 (p) REVERT: A 346 GLU cc_start: 0.7824 (mp0) cc_final: 0.7492 (mp0) REVERT: A 348 PHE cc_start: 0.8814 (t80) cc_final: 0.8562 (t80) REVERT: A 351 LYS cc_start: 0.8316 (tttp) cc_final: 0.7719 (tppt) REVERT: A 355 ARG cc_start: 0.8330 (ttm110) cc_final: 0.7858 (ttm110) REVERT: A 366 THR cc_start: 0.8604 (p) cc_final: 0.8399 (p) REVERT: A 368 LYS cc_start: 0.8814 (mtpt) cc_final: 0.8477 (mtpt) REVERT: A 369 ARG cc_start: 0.9110 (ptm-80) cc_final: 0.8699 (ptm-80) REVERT: A 370 LEU cc_start: 0.8946 (tt) cc_final: 0.8510 (tt) REVERT: A 379 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7332 (mtp85) REVERT: A 382 HIS cc_start: 0.7386 (t-90) cc_final: 0.7073 (t-90) REVERT: A 409 TYR cc_start: 0.8679 (t80) cc_final: 0.8235 (t80) REVERT: A 426 TYR cc_start: 0.7168 (p90) cc_final: 0.6760 (p90) REVERT: A 482 LYS cc_start: 0.7814 (mmmm) cc_final: 0.7120 (mmmm) REVERT: A 489 ASN cc_start: 0.7137 (p0) cc_final: 0.6829 (p0) REVERT: A 502 LEU cc_start: 0.9087 (pp) cc_final: 0.8642 (pp) REVERT: A 505 LYS cc_start: 0.9260 (tmtt) cc_final: 0.8878 (tmtt) REVERT: A 516 VAL cc_start: 0.8821 (m) cc_final: 0.8272 (p) REVERT: A 519 ASN cc_start: 0.7752 (m110) cc_final: 0.7468 (m110) REVERT: A 520 ASN cc_start: 0.8861 (m-40) cc_final: 0.8571 (m-40) REVERT: A 525 ASN cc_start: 0.6853 (m110) cc_final: 0.6338 (m110) REVERT: A 565 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7602 (mt-10) REVERT: A 569 ASN cc_start: 0.7143 (m110) cc_final: 0.6778 (m110) REVERT: A 603 MET cc_start: 0.8435 (mtm) cc_final: 0.8225 (mtm) REVERT: B 136 LYS cc_start: 0.7831 (mmpt) cc_final: 0.7135 (mmpt) REVERT: B 154 VAL cc_start: 0.8294 (p) cc_final: 0.7927 (p) REVERT: C 13 LEU cc_start: 0.8703 (tp) cc_final: 0.8299 (tp) REVERT: C 15 GLN cc_start: 0.8389 (pp30) cc_final: 0.8068 (pp30) REVERT: C 30 LYS cc_start: 0.8051 (mttt) cc_final: 0.7824 (mttt) REVERT: C 32 LEU cc_start: 0.7895 (mt) cc_final: 0.7624 (mt) REVERT: C 41 TYR cc_start: 0.7212 (p90) cc_final: 0.6967 (p90) REVERT: C 53 LYS cc_start: 0.7210 (mppt) cc_final: 0.6380 (tppt) REVERT: C 71 ASN cc_start: 0.7555 (m110) cc_final: 0.7352 (m110) REVERT: C 84 GLN cc_start: 0.7935 (mp10) cc_final: 0.7497 (mp10) REVERT: C 95 LYS cc_start: 0.9133 (mppt) cc_final: 0.8700 (mppt) REVERT: C 98 MET cc_start: 0.7441 (ttm) cc_final: 0.7112 (ttm) REVERT: C 128 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7014 (mt-10) REVERT: C 144 GLU cc_start: 0.7133 (tp30) cc_final: 0.6821 (tp30) REVERT: C 159 ASP cc_start: 0.7541 (t0) cc_final: 0.7001 (t0) REVERT: C 164 MET cc_start: 0.8584 (ppp) cc_final: 0.8315 (ppp) REVERT: C 199 TYR cc_start: 0.8104 (t80) cc_final: 0.7670 (t80) REVERT: C 204 TYR cc_start: 0.7678 (m-80) cc_final: 0.7384 (m-10) REVERT: C 218 GLN cc_start: 0.7451 (mt0) cc_final: 0.6935 (mt0) REVERT: C 225 CYS cc_start: 0.8530 (m) cc_final: 0.8310 (m) REVERT: C 232 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7974 (mp) REVERT: C 236 LYS cc_start: 0.8737 (mppt) cc_final: 0.8153 (mppt) REVERT: C 244 GLN cc_start: 0.6083 (tp-100) cc_final: 0.5769 (tp40) REVERT: C 263 ARG cc_start: 0.8319 (ptt180) cc_final: 0.6934 (ptt180) REVERT: C 267 ARG cc_start: 0.7989 (ppt170) cc_final: 0.7570 (ppt170) REVERT: C 306 MET cc_start: 0.7991 (tmm) cc_final: 0.7447 (tmm) REVERT: C 307 LEU cc_start: 0.8822 (mt) cc_final: 0.8584 (mt) REVERT: C 316 MET cc_start: 0.7243 (mtt) cc_final: 0.6913 (mtt) REVERT: C 323 GLN cc_start: 0.8785 (mt0) cc_final: 0.8466 (mm110) REVERT: C 351 LYS cc_start: 0.9062 (ttmm) cc_final: 0.8728 (tttm) REVERT: C 365 ASP cc_start: 0.7915 (p0) cc_final: 0.7590 (p0) REVERT: C 406 TRP cc_start: 0.8817 (t-100) cc_final: 0.8368 (t-100) REVERT: C 410 GLU cc_start: 0.8311 (tt0) cc_final: 0.7991 (tt0) REVERT: C 438 GLU cc_start: 0.8045 (mm-30) cc_final: 0.6551 (tp30) REVERT: C 442 CYS cc_start: 0.6794 (p) cc_final: 0.6479 (m) REVERT: C 445 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7518 (mttm) REVERT: C 449 SER cc_start: 0.8612 (t) cc_final: 0.8406 (t) REVERT: C 454 GLU cc_start: 0.7927 (pt0) cc_final: 0.7706 (pt0) REVERT: C 476 PHE cc_start: 0.7964 (m-80) cc_final: 0.7674 (m-80) REVERT: C 486 LYS cc_start: 0.6100 (mttt) cc_final: 0.5674 (mmtp) REVERT: C 504 GLU cc_start: 0.8526 (tp30) cc_final: 0.8077 (tp30) REVERT: C 518 ILE cc_start: 0.8942 (mm) cc_final: 0.8488 (mm) REVERT: C 522 CYS cc_start: 0.8857 (m) cc_final: 0.8628 (m) REVERT: C 550 LYS cc_start: 0.8406 (mttt) cc_final: 0.8153 (mttt) REVERT: C 557 LEU cc_start: 0.8940 (mm) cc_final: 0.8583 (mm) REVERT: C 566 LYS cc_start: 0.8713 (pttp) cc_final: 0.8323 (pttp) REVERT: C 582 LEU cc_start: 0.8882 (mt) cc_final: 0.8455 (mt) REVERT: C 584 HIS cc_start: 0.8496 (m90) cc_final: 0.8230 (m90) REVERT: C 590 LYS cc_start: 0.8532 (tttt) cc_final: 0.8070 (tttt) REVERT: C 603 MET cc_start: 0.7618 (mtt) cc_final: 0.7379 (mtt) REVERT: C 606 LEU cc_start: 0.8718 (mp) cc_final: 0.8474 (mp) REVERT: D 18 ASP cc_start: 0.6442 (m-30) cc_final: 0.6045 (m-30) REVERT: D 78 ASN cc_start: 0.9027 (t0) cc_final: 0.8655 (t0) REVERT: D 87 GLU cc_start: 0.8112 (tp30) cc_final: 0.7863 (mm-30) REVERT: D 89 GLN cc_start: 0.8869 (mm110) cc_final: 0.8655 (mm110) REVERT: D 103 HIS cc_start: 0.6725 (m-70) cc_final: 0.6442 (m-70) REVERT: D 157 LEU cc_start: 0.8649 (mm) cc_final: 0.8258 (mm) outliers start: 3 outliers final: 0 residues processed: 466 average time/residue: 0.1251 time to fit residues: 82.6698 Evaluate side-chains 433 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 432 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 80 optimal weight: 0.0270 chunk 112 optimal weight: 1.9990 chunk 118 optimal weight: 0.0980 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 39 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.156703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.121686 restraints weight = 30728.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.126139 restraints weight = 17644.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129244 restraints weight = 11529.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.131383 restraints weight = 8173.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.132915 restraints weight = 6251.619| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14205 Z= 0.134 Angle : 0.687 10.483 19562 Z= 0.360 Chirality : 0.042 0.172 2195 Planarity : 0.004 0.057 2244 Dihedral : 21.165 167.916 2554 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.14 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.21), residues: 1535 helix: 0.12 (0.21), residues: 584 sheet: -0.43 (0.36), residues: 233 loop : -1.63 (0.23), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 472 TYR 0.031 0.002 TYR A 41 PHE 0.024 0.001 PHE A 589 TRP 0.030 0.002 TRP A 259 HIS 0.008 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00287 (14204) covalent geometry : angle 0.68667 (19562) hydrogen bonds : bond 0.04157 ( 580) hydrogen bonds : angle 5.08599 ( 1605) Misc. bond : bond 0.00083 ( 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 464 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.485 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: 0.9102 (mttt) cc_final: 0.8833 (mttp) REVERT: A 65 ASP cc_start: 0.8588 (t70) cc_final: 0.8189 (t0) REVERT: A 66 PHE cc_start: 0.7184 (m-80) cc_final: 0.6858 (m-80) REVERT: A 119 ASP cc_start: 0.8812 (p0) cc_final: 0.8558 (p0) REVERT: A 181 ARG cc_start: 0.8691 (ttp80) cc_final: 0.8183 (ttp80) REVERT: A 226 VAL cc_start: 0.8788 (p) cc_final: 0.8474 (p) REVERT: A 228 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7678 (ttp80) REVERT: A 231 LYS cc_start: 0.9019 (mptt) cc_final: 0.8708 (mptt) REVERT: A 236 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8616 (tppt) REVERT: A 255 LEU cc_start: 0.7743 (mt) cc_final: 0.7438 (mt) REVERT: A 290 ARG cc_start: 0.8469 (ppt170) cc_final: 0.8039 (pmt-80) REVERT: A 293 LYS cc_start: 0.7993 (pttm) cc_final: 0.7370 (pttm) REVERT: A 297 ARG cc_start: 0.6164 (ptm160) cc_final: 0.5882 (ptm160) REVERT: A 305 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8099 (tp30) REVERT: A 324 THR cc_start: 0.8083 (p) cc_final: 0.7849 (p) REVERT: A 346 GLU cc_start: 0.7840 (mp0) cc_final: 0.7526 (mp0) REVERT: A 348 PHE cc_start: 0.8833 (t80) cc_final: 0.8585 (t80) REVERT: A 351 LYS cc_start: 0.8374 (tttp) cc_final: 0.7640 (ttmm) REVERT: A 355 ARG cc_start: 0.8350 (ttm110) cc_final: 0.7710 (ttm110) REVERT: A 368 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8480 (mtpt) REVERT: A 370 LEU cc_start: 0.8950 (tt) cc_final: 0.8738 (tt) REVERT: A 379 ARG cc_start: 0.7766 (mtp85) cc_final: 0.7451 (mtp85) REVERT: A 382 HIS cc_start: 0.7309 (t-90) cc_final: 0.6988 (t-90) REVERT: A 398 GLU cc_start: 0.7361 (pm20) cc_final: 0.7143 (pm20) REVERT: A 409 TYR cc_start: 0.8684 (t80) cc_final: 0.8298 (t80) REVERT: A 426 TYR cc_start: 0.7094 (p90) cc_final: 0.6733 (p90) REVERT: A 482 LYS cc_start: 0.7817 (mmmm) cc_final: 0.7158 (mmmm) REVERT: A 489 ASN cc_start: 0.6944 (p0) cc_final: 0.6730 (p0) REVERT: A 502 LEU cc_start: 0.9077 (pp) cc_final: 0.8601 (pp) REVERT: A 505 LYS cc_start: 0.9253 (tmtt) cc_final: 0.8902 (tmtt) REVERT: A 516 VAL cc_start: 0.8799 (m) cc_final: 0.8236 (p) REVERT: A 519 ASN cc_start: 0.7732 (m110) cc_final: 0.7476 (m110) REVERT: A 520 ASN cc_start: 0.8847 (m-40) cc_final: 0.8521 (m-40) REVERT: A 525 ASN cc_start: 0.6710 (m110) cc_final: 0.6167 (m110) REVERT: A 560 ILE cc_start: 0.8224 (mt) cc_final: 0.7989 (pt) REVERT: A 565 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7584 (mt-10) REVERT: A 569 ASN cc_start: 0.7166 (m110) cc_final: 0.6810 (m110) REVERT: A 603 MET cc_start: 0.8393 (mtm) cc_final: 0.8171 (mtm) REVERT: B 106 CYS cc_start: 0.7372 (t) cc_final: 0.7137 (t) REVERT: B 134 ASP cc_start: 0.6665 (p0) cc_final: 0.6459 (p0) REVERT: B 136 LYS cc_start: 0.7918 (mmpt) cc_final: 0.7499 (mmpt) REVERT: C 15 GLN cc_start: 0.8408 (pp30) cc_final: 0.8117 (pp30) REVERT: C 30 LYS cc_start: 0.8105 (mttt) cc_final: 0.7881 (mttt) REVERT: C 32 LEU cc_start: 0.7931 (mt) cc_final: 0.7672 (mt) REVERT: C 41 TYR cc_start: 0.7156 (p90) cc_final: 0.6934 (p90) REVERT: C 53 LYS cc_start: 0.7136 (mppt) cc_final: 0.6311 (tppt) REVERT: C 84 GLN cc_start: 0.7912 (mp10) cc_final: 0.7065 (mp10) REVERT: C 89 LYS cc_start: 0.8435 (mppt) cc_final: 0.8098 (mppt) REVERT: C 95 LYS cc_start: 0.9119 (mppt) cc_final: 0.8672 (mppt) REVERT: C 98 MET cc_start: 0.7453 (ttm) cc_final: 0.7066 (ttm) REVERT: C 139 LYS cc_start: 0.7513 (tmmt) cc_final: 0.7250 (ptmm) REVERT: C 144 GLU cc_start: 0.7130 (tp30) cc_final: 0.6819 (tp30) REVERT: C 152 PHE cc_start: 0.7538 (p90) cc_final: 0.7333 (p90) REVERT: C 159 ASP cc_start: 0.7482 (t0) cc_final: 0.6914 (t0) REVERT: C 164 MET cc_start: 0.8570 (ppp) cc_final: 0.8301 (ppp) REVERT: C 199 TYR cc_start: 0.8064 (t80) cc_final: 0.7661 (t80) REVERT: C 204 TYR cc_start: 0.7743 (m-80) cc_final: 0.7428 (m-10) REVERT: C 218 GLN cc_start: 0.7486 (mt0) cc_final: 0.6921 (mt0) REVERT: C 222 LEU cc_start: 0.7860 (tp) cc_final: 0.7651 (tp) REVERT: C 225 CYS cc_start: 0.8538 (m) cc_final: 0.8328 (m) REVERT: C 236 LYS cc_start: 0.8724 (mppt) cc_final: 0.8161 (mppt) REVERT: C 244 GLN cc_start: 0.6050 (tp-100) cc_final: 0.5757 (tp40) REVERT: C 263 ARG cc_start: 0.8287 (ptt180) cc_final: 0.6876 (ptt180) REVERT: C 267 ARG cc_start: 0.8047 (ppt170) cc_final: 0.7673 (ppt170) REVERT: C 292 GLU cc_start: 0.8399 (pm20) cc_final: 0.8114 (pm20) REVERT: C 306 MET cc_start: 0.7989 (tmm) cc_final: 0.7435 (tmm) REVERT: C 307 LEU cc_start: 0.8863 (mt) cc_final: 0.8599 (mt) REVERT: C 316 MET cc_start: 0.7258 (mtt) cc_final: 0.6933 (mtt) REVERT: C 323 GLN cc_start: 0.8763 (mt0) cc_final: 0.8456 (mm110) REVERT: C 351 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8708 (tttm) REVERT: C 365 ASP cc_start: 0.7846 (p0) cc_final: 0.7562 (p0) REVERT: C 382 HIS cc_start: 0.8115 (t70) cc_final: 0.7845 (t-90) REVERT: C 406 TRP cc_start: 0.8759 (t-100) cc_final: 0.8072 (t-100) REVERT: C 410 GLU cc_start: 0.8344 (tt0) cc_final: 0.8044 (tt0) REVERT: C 442 CYS cc_start: 0.6566 (p) cc_final: 0.6279 (m) REVERT: C 449 SER cc_start: 0.8608 (t) cc_final: 0.8402 (t) REVERT: C 476 PHE cc_start: 0.8001 (m-80) cc_final: 0.7710 (m-80) REVERT: C 504 GLU cc_start: 0.8451 (tp30) cc_final: 0.8065 (tp30) REVERT: C 522 CYS cc_start: 0.8765 (m) cc_final: 0.8551 (m) REVERT: C 549 TYR cc_start: 0.7623 (m-80) cc_final: 0.7394 (m-80) REVERT: C 550 LYS cc_start: 0.8379 (mttt) cc_final: 0.8121 (mttt) REVERT: C 557 LEU cc_start: 0.8928 (mm) cc_final: 0.8564 (mm) REVERT: C 566 LYS cc_start: 0.8728 (pttp) cc_final: 0.8323 (pttp) REVERT: C 582 LEU cc_start: 0.8906 (mt) cc_final: 0.8505 (mt) REVERT: C 584 HIS cc_start: 0.8513 (m90) cc_final: 0.8260 (m90) REVERT: C 590 LYS cc_start: 0.8457 (tttt) cc_final: 0.7921 (tttt) REVERT: C 603 MET cc_start: 0.7661 (mtt) cc_final: 0.7387 (mtt) REVERT: C 606 LEU cc_start: 0.8718 (mp) cc_final: 0.8463 (mp) REVERT: D 78 ASN cc_start: 0.8976 (t0) cc_final: 0.8557 (t0) REVERT: D 87 GLU cc_start: 0.8123 (tp30) cc_final: 0.7895 (mm-30) REVERT: D 89 GLN cc_start: 0.8914 (mm110) cc_final: 0.8708 (mm110) REVERT: D 103 HIS cc_start: 0.6730 (m-70) cc_final: 0.6426 (m-70) outliers start: 0 outliers final: 0 residues processed: 464 average time/residue: 0.1311 time to fit residues: 85.4172 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 : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 2 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN C 357 GLN C 415 HIS ** 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 = 0.4127 r_free = 0.4127 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120777 restraints weight = 30406.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.125203 restraints weight = 17567.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.128226 restraints weight = 11460.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130336 restraints weight = 8164.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.131876 restraints weight = 6245.139| |-----------------------------------------------------------------------------| r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14205 Z= 0.144 Angle : 0.698 10.118 19562 Z= 0.367 Chirality : 0.042 0.175 2195 Planarity : 0.005 0.075 2244 Dihedral : 21.160 168.854 2554 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.95 % Favored : 91.99 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1535 helix: 0.11 (0.21), residues: 585 sheet: -0.43 (0.36), residues: 233 loop : -1.63 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 472 TYR 0.023 0.002 TYR A 595 PHE 0.067 0.001 PHE A 589 TRP 0.019 0.002 TRP A 259 HIS 0.009 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00306 (14204) covalent geometry : angle 0.69783 (19562) hydrogen bonds : bond 0.04213 ( 580) hydrogen bonds : angle 5.08965 ( 1605) Misc. bond : bond 0.00078 ( 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 452 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 0.370 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: 0.8840 (mttp) REVERT: A 62 MET cc_start: 0.5861 (tmm) cc_final: 0.5640 (tmm) REVERT: A 65 ASP cc_start: 0.8609 (t70) cc_final: 0.8188 (t0) REVERT: A 66 PHE cc_start: 0.7172 (m-80) cc_final: 0.6775 (m-80) REVERT: A 181 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8196 (ttp80) REVERT: A 226 VAL cc_start: 0.8823 (p) cc_final: 0.8496 (p) REVERT: A 228 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.7982 (mtm180) REVERT: A 231 LYS cc_start: 0.9022 (mptt) cc_final: 0.8719 (mptt) REVERT: A 246 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6643 (tmtt) REVERT: A 255 LEU cc_start: 0.7724 (mt) cc_final: 0.7312 (mt) REVERT: A 260 ASP cc_start: 0.7820 (p0) cc_final: 0.7607 (p0) REVERT: A 290 ARG cc_start: 0.8479 (ppt170) cc_final: 0.8034 (pmt-80) REVERT: A 293 LYS cc_start: 0.7972 (pttm) cc_final: 0.7352 (pttm) REVERT: A 305 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8202 (tp30) REVERT: A 323 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 324 THR cc_start: 0.7979 (p) cc_final: 0.7697 (p) REVERT: A 346 GLU cc_start: 0.7835 (mp0) cc_final: 0.7544 (mp0) REVERT: A 348 PHE cc_start: 0.8850 (t80) cc_final: 0.8605 (t80) REVERT: A 351 LYS cc_start: 0.8404 (tttp) cc_final: 0.7613 (ttmm) REVERT: A 355 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7658 (ttm110) REVERT: A 366 THR cc_start: 0.8505 (p) cc_final: 0.8293 (p) REVERT: A 368 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8468 (mtpt) REVERT: A 369 ARG cc_start: 0.9091 (ptm-80) cc_final: 0.8685 (ptm-80) REVERT: A 370 LEU cc_start: 0.8981 (tt) cc_final: 0.8447 (tt) REVERT: A 379 ARG cc_start: 0.7793 (mtp85) cc_final: 0.7228 (mtp85) REVERT: A 382 HIS cc_start: 0.7379 (t-90) cc_final: 0.7029 (t-90) REVERT: A 398 GLU cc_start: 0.7368 (pm20) cc_final: 0.7046 (pm20) REVERT: A 409 TYR cc_start: 0.8695 (t80) cc_final: 0.8352 (t80) REVERT: A 426 TYR cc_start: 0.7090 (p90) cc_final: 0.6772 (p90) REVERT: A 482 LYS cc_start: 0.7816 (mmmm) cc_final: 0.7190 (mmmm) REVERT: A 489 ASN cc_start: 0.6837 (p0) cc_final: 0.6600 (p0) REVERT: A 502 LEU cc_start: 0.9069 (pp) cc_final: 0.8584 (pp) REVERT: A 516 VAL cc_start: 0.8806 (m) cc_final: 0.8245 (p) REVERT: A 519 ASN cc_start: 0.7754 (m110) cc_final: 0.7463 (m110) REVERT: A 520 ASN cc_start: 0.8838 (m-40) cc_final: 0.8501 (m-40) REVERT: A 525 ASN cc_start: 0.6812 (m110) cc_final: 0.6276 (m110) REVERT: A 560 ILE cc_start: 0.8236 (mt) cc_final: 0.7993 (pt) REVERT: A 565 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7597 (mt-10) REVERT: A 569 ASN cc_start: 0.7193 (m110) cc_final: 0.6838 (m110) REVERT: A 590 LYS cc_start: 0.8901 (mptt) cc_final: 0.8550 (mptt) REVERT: B 106 CYS cc_start: 0.7329 (t) cc_final: 0.7109 (t) REVERT: B 136 LYS cc_start: 0.7891 (mmpt) cc_final: 0.7135 (mmpt) REVERT: C 15 GLN cc_start: 0.8420 (pp30) cc_final: 0.8101 (pp30) REVERT: C 30 LYS cc_start: 0.8096 (mttt) cc_final: 0.7887 (mttt) REVERT: C 32 LEU cc_start: 0.7894 (mt) cc_final: 0.7617 (mt) REVERT: C 41 TYR cc_start: 0.7186 (p90) cc_final: 0.6922 (p90) REVERT: C 53 LYS cc_start: 0.6846 (mppt) cc_final: 0.6251 (mppt) REVERT: C 84 GLN cc_start: 0.7934 (mp10) cc_final: 0.7075 (mp10) REVERT: C 95 LYS cc_start: 0.9136 (mppt) cc_final: 0.8710 (mppt) REVERT: C 98 MET cc_start: 0.7508 (ttm) cc_final: 0.7110 (ttm) REVERT: C 128 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7055 (mt-10) REVERT: C 139 LYS cc_start: 0.7550 (tmmt) cc_final: 0.6976 (pttp) REVERT: C 144 GLU cc_start: 0.7137 (tp30) cc_final: 0.6822 (tp30) REVERT: C 152 PHE cc_start: 0.7560 (p90) cc_final: 0.7335 (p90) REVERT: C 159 ASP cc_start: 0.7462 (t0) cc_final: 0.6859 (t0) REVERT: C 164 MET cc_start: 0.8508 (ppp) cc_final: 0.8246 (ppp) REVERT: C 199 TYR cc_start: 0.8046 (t80) cc_final: 0.7713 (t80) REVERT: C 204 TYR cc_start: 0.7761 (m-80) cc_final: 0.7429 (m-10) REVERT: C 218 GLN cc_start: 0.7511 (mt0) cc_final: 0.6985 (mt0) REVERT: C 222 LEU cc_start: 0.7867 (tp) cc_final: 0.7647 (tp) REVERT: C 225 CYS cc_start: 0.8534 (m) cc_final: 0.8318 (m) REVERT: C 236 LYS cc_start: 0.8741 (mppt) cc_final: 0.8193 (mppt) REVERT: C 244 GLN cc_start: 0.6077 (tp-100) cc_final: 0.5853 (tp40) REVERT: C 263 ARG cc_start: 0.8275 (ptt180) cc_final: 0.6905 (ptt180) REVERT: C 267 ARG cc_start: 0.7999 (ppt170) cc_final: 0.7570 (ppt170) REVERT: C 268 GLU cc_start: 0.8280 (pp20) cc_final: 0.5971 (tm-30) REVERT: C 292 GLU cc_start: 0.8433 (pm20) cc_final: 0.8186 (pm20) REVERT: C 306 MET cc_start: 0.8018 (tmm) cc_final: 0.7526 (tmm) REVERT: C 307 LEU cc_start: 0.8876 (mt) cc_final: 0.8637 (mt) REVERT: C 316 MET cc_start: 0.7280 (mtt) cc_final: 0.6995 (mtt) REVERT: C 323 GLN cc_start: 0.8771 (mt0) cc_final: 0.8493 (mm110) REVERT: C 344 TYR cc_start: 0.8907 (m-10) cc_final: 0.8563 (m-10) REVERT: C 351 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8604 (mtpp) REVERT: C 365 ASP cc_start: 0.7832 (p0) cc_final: 0.7578 (p0) REVERT: C 367 VAL cc_start: 0.8948 (t) cc_final: 0.8643 (p) REVERT: C 382 HIS cc_start: 0.8093 (t70) cc_final: 0.7817 (t-90) REVERT: C 406 TRP cc_start: 0.8787 (t-100) cc_final: 0.8507 (t-100) REVERT: C 410 GLU cc_start: 0.8334 (tt0) cc_final: 0.8072 (tt0) REVERT: C 438 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7449 (tp30) REVERT: C 449 SER cc_start: 0.8608 (t) cc_final: 0.8396 (t) REVERT: C 454 GLU cc_start: 0.7904 (pt0) cc_final: 0.7681 (pt0) REVERT: C 476 PHE cc_start: 0.7970 (m-80) cc_final: 0.7715 (m-80) REVERT: C 504 GLU cc_start: 0.8375 (tp30) cc_final: 0.7909 (tp30) REVERT: C 549 TYR cc_start: 0.7611 (m-80) cc_final: 0.7357 (m-80) REVERT: C 550 LYS cc_start: 0.8370 (mttt) cc_final: 0.8144 (mttt) REVERT: C 552 ASP cc_start: 0.8042 (t70) cc_final: 0.7831 (t70) REVERT: C 557 LEU cc_start: 0.8917 (mm) cc_final: 0.8562 (mm) REVERT: C 566 LYS cc_start: 0.8740 (pttp) cc_final: 0.8334 (pttp) REVERT: C 582 LEU cc_start: 0.8876 (mt) cc_final: 0.8482 (mt) REVERT: C 584 HIS cc_start: 0.8496 (m90) cc_final: 0.8255 (m90) REVERT: C 590 LYS cc_start: 0.8492 (tttt) cc_final: 0.8032 (tttt) REVERT: C 603 MET cc_start: 0.7659 (mtt) cc_final: 0.7400 (mtt) REVERT: C 606 LEU cc_start: 0.8722 (mp) cc_final: 0.8503 (mp) REVERT: D 18 ASP cc_start: 0.6409 (m-30) cc_final: 0.5781 (m-30) REVERT: D 78 ASN cc_start: 0.8981 (t0) cc_final: 0.8603 (t0) REVERT: D 87 GLU cc_start: 0.8146 (tp30) cc_final: 0.7893 (mm-30) REVERT: D 89 GLN cc_start: 0.8870 (mm110) cc_final: 0.8668 (mm110) REVERT: D 103 HIS cc_start: 0.6774 (m-70) cc_final: 0.6516 (m-70) REVERT: D 157 LEU cc_start: 0.8582 (mm) cc_final: 0.8322 (mm) outliers start: 0 outliers final: 0 residues processed: 452 average time/residue: 0.1290 time to fit residues: 82.2195 Evaluate side-chains 423 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 423 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 71 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 146 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 HIS ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.155005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.120350 restraints weight = 30534.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.124812 restraints weight = 17659.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.127808 restraints weight = 11550.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129919 restraints weight = 8243.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.131172 restraints weight = 6300.894| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.3860 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= 0.149 Angle : 0.707 12.888 19562 Z= 0.371 Chirality : 0.042 0.172 2195 Planarity : 0.005 0.065 2244 Dihedral : 21.165 169.332 2554 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.66 % Favored : 91.27 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.21), residues: 1535 helix: 0.12 (0.21), residues: 580 sheet: -0.43 (0.34), residues: 239 loop : -1.67 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 46 TYR 0.027 0.002 TYR A 41 PHE 0.025 0.001 PHE A 589 TRP 0.021 0.003 TRP D 14 HIS 0.018 0.001 HIS A 594 Details of bonding type rmsd covalent geometry : bond 0.00319 (14204) covalent geometry : angle 0.70745 (19562) hydrogen bonds : bond 0.04265 ( 580) hydrogen bonds : angle 5.11186 ( 1605) Misc. bond : bond 0.00080 ( 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 453 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.480 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: 0.9118 (mttt) cc_final: 0.8859 (mttp) REVERT: A 65 ASP cc_start: 0.8611 (t70) cc_final: 0.8169 (t0) REVERT: A 66 PHE cc_start: 0.7150 (m-80) cc_final: 0.6750 (m-80) REVERT: A 181 ARG cc_start: 0.8692 (ttp80) cc_final: 0.8168 (ttp80) REVERT: A 226 VAL cc_start: 0.8846 (p) cc_final: 0.8504 (p) REVERT: A 228 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7675 (ttp80) REVERT: A 231 LYS cc_start: 0.9050 (mptt) cc_final: 0.8720 (mptt) REVERT: A 246 LYS cc_start: 0.6946 (tmtt) cc_final: 0.6657 (tmtt) REVERT: A 255 LEU cc_start: 0.7758 (mt) cc_final: 0.7335 (mt) REVERT: A 260 ASP cc_start: 0.7837 (p0) cc_final: 0.7522 (p0) REVERT: A 293 LYS cc_start: 0.7999 (pttm) cc_final: 0.7397 (pttm) REVERT: A 305 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8202 (tp30) REVERT: A 316 MET cc_start: 0.7271 (tmm) cc_final: 0.7016 (tpp) REVERT: A 320 HIS cc_start: 0.7164 (t70) cc_final: 0.6669 (t70) REVERT: A 323 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8101 (tm-30) REVERT: A 324 THR cc_start: 0.8022 (p) cc_final: 0.7630 (p) REVERT: A 346 GLU cc_start: 0.7835 (mp0) cc_final: 0.7551 (mp0) REVERT: A 348 PHE cc_start: 0.8870 (t80) cc_final: 0.8609 (t80) REVERT: A 351 LYS cc_start: 0.8460 (tttp) cc_final: 0.7866 (tttp) REVERT: A 355 ARG cc_start: 0.8401 (ttm110) cc_final: 0.7705 (ttm110) REVERT: A 368 LYS cc_start: 0.8803 (mtpt) cc_final: 0.8460 (mtpt) REVERT: A 370 LEU cc_start: 0.8972 (tt) cc_final: 0.8716 (tt) REVERT: A 379 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7287 (mtp85) REVERT: A 382 HIS cc_start: 0.7432 (t-90) cc_final: 0.7057 (t-90) REVERT: A 394 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8204 (ttpt) REVERT: A 409 TYR cc_start: 0.8705 (t80) cc_final: 0.8327 (t80) REVERT: A 416 PHE cc_start: 0.8768 (t80) cc_final: 0.8552 (t80) REVERT: A 426 TYR cc_start: 0.7111 (p90) cc_final: 0.6778 (p90) REVERT: A 456 MET cc_start: 0.8407 (mtm) cc_final: 0.7861 (mtm) REVERT: A 482 LYS cc_start: 0.7780 (mmmm) cc_final: 0.7170 (mmmm) REVERT: A 489 ASN cc_start: 0.6820 (p0) cc_final: 0.6590 (p0) REVERT: A 502 LEU cc_start: 0.9074 (pp) cc_final: 0.8585 (pp) REVERT: A 516 VAL cc_start: 0.8814 (m) cc_final: 0.8259 (p) REVERT: A 519 ASN cc_start: 0.7729 (m110) cc_final: 0.7459 (m110) REVERT: A 520 ASN cc_start: 0.8835 (m-40) cc_final: 0.8492 (m-40) REVERT: A 525 ASN cc_start: 0.6971 (m110) cc_final: 0.6448 (m110) REVERT: A 560 ILE cc_start: 0.8245 (mt) cc_final: 0.7969 (pt) REVERT: A 565 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7606 (mt-10) REVERT: A 569 ASN cc_start: 0.7130 (m110) cc_final: 0.6752 (m110) REVERT: A 585 THR cc_start: 0.7925 (t) cc_final: 0.7607 (t) REVERT: A 590 LYS cc_start: 0.8916 (mptt) cc_final: 0.8253 (mmmt) REVERT: A 594 HIS cc_start: 0.8345 (m90) cc_final: 0.8118 (m90) REVERT: B 106 CYS cc_start: 0.7347 (t) cc_final: 0.7135 (t) REVERT: B 134 ASP cc_start: 0.6879 (p0) cc_final: 0.6656 (p0) REVERT: B 136 LYS cc_start: 0.7827 (mmpt) cc_final: 0.7186 (mmpt) REVERT: C 30 LYS cc_start: 0.8141 (mttt) cc_final: 0.7919 (mttt) REVERT: C 32 LEU cc_start: 0.7947 (mt) cc_final: 0.7665 (mt) REVERT: C 41 TYR cc_start: 0.7182 (p90) cc_final: 0.6959 (p90) REVERT: C 53 LYS cc_start: 0.6857 (mppt) cc_final: 0.6210 (mppt) REVERT: C 84 GLN cc_start: 0.7968 (mp10) cc_final: 0.7105 (mp10) REVERT: C 89 LYS cc_start: 0.8339 (mppt) cc_final: 0.7977 (mppt) REVERT: C 95 LYS cc_start: 0.9130 (mppt) cc_final: 0.8665 (mppt) REVERT: C 98 MET cc_start: 0.7492 (ttm) cc_final: 0.7115 (ttm) REVERT: C 128 GLU cc_start: 0.7572 (mt-10) cc_final: 0.6953 (mt-10) REVERT: C 139 LYS cc_start: 0.7609 (tmmt) cc_final: 0.7344 (ptmm) REVERT: C 144 GLU cc_start: 0.7142 (tp30) cc_final: 0.6614 (tm-30) REVERT: C 159 ASP cc_start: 0.7476 (t0) cc_final: 0.6850 (t0) REVERT: C 164 MET cc_start: 0.8517 (ppp) cc_final: 0.8252 (ppp) REVERT: C 204 TYR cc_start: 0.7768 (m-80) cc_final: 0.7405 (m-10) REVERT: C 218 GLN cc_start: 0.7489 (mt0) cc_final: 0.6964 (mt0) REVERT: C 225 CYS cc_start: 0.8541 (m) cc_final: 0.8305 (m) REVERT: C 236 LYS cc_start: 0.8765 (mppt) cc_final: 0.8213 (mppt) REVERT: C 244 GLN cc_start: 0.6080 (tp-100) cc_final: 0.5775 (tp-100) REVERT: C 263 ARG cc_start: 0.8280 (ptt180) cc_final: 0.6930 (ptt180) REVERT: C 267 ARG cc_start: 0.7996 (ppt170) cc_final: 0.7602 (ppt170) REVERT: C 268 GLU cc_start: 0.8278 (pp20) cc_final: 0.7806 (pp20) REVERT: C 273 PHE cc_start: 0.8254 (m-10) cc_final: 0.7948 (m-10) REVERT: C 281 LYS cc_start: 0.6991 (mmmt) cc_final: 0.6785 (mmmt) REVERT: C 305 GLU cc_start: 0.8054 (tp30) cc_final: 0.7763 (tp30) REVERT: C 306 MET cc_start: 0.8035 (tmm) cc_final: 0.7619 (tmm) REVERT: C 307 LEU cc_start: 0.8910 (mt) cc_final: 0.8692 (mt) REVERT: C 308 ARG cc_start: 0.8600 (ttp-170) cc_final: 0.8116 (ttm-80) REVERT: C 316 MET cc_start: 0.7379 (mtt) cc_final: 0.7031 (mtt) REVERT: C 344 TYR cc_start: 0.8873 (m-10) cc_final: 0.8664 (m-10) REVERT: C 351 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8673 (tttm) REVERT: C 362 TYR cc_start: 0.8114 (m-10) cc_final: 0.7880 (m-10) REVERT: C 365 ASP cc_start: 0.7855 (p0) cc_final: 0.7584 (p0) REVERT: C 367 VAL cc_start: 0.8954 (t) cc_final: 0.8633 (p) REVERT: C 410 GLU cc_start: 0.8345 (tt0) cc_final: 0.8092 (tt0) REVERT: C 449 SER cc_start: 0.8602 (t) cc_final: 0.8393 (t) REVERT: C 476 PHE cc_start: 0.7949 (m-80) cc_final: 0.7692 (m-80) REVERT: C 504 GLU cc_start: 0.8455 (tp30) cc_final: 0.7932 (tp30) REVERT: C 536 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7464 (ttmt) REVERT: C 549 TYR cc_start: 0.7605 (m-80) cc_final: 0.7317 (m-80) REVERT: C 550 LYS cc_start: 0.8380 (mttt) cc_final: 0.8170 (mttt) REVERT: C 557 LEU cc_start: 0.8975 (mm) cc_final: 0.8735 (mm) REVERT: C 566 LYS cc_start: 0.8742 (pttp) cc_final: 0.8324 (pttp) REVERT: C 584 HIS cc_start: 0.8509 (m90) cc_final: 0.8247 (m90) REVERT: C 590 LYS cc_start: 0.8498 (tttt) cc_final: 0.8053 (tttt) REVERT: C 603 MET cc_start: 0.7617 (mtt) cc_final: 0.7363 (mtt) REVERT: C 606 LEU cc_start: 0.8730 (mp) cc_final: 0.8515 (mp) REVERT: D 78 ASN cc_start: 0.9004 (t0) cc_final: 0.8608 (t0) REVERT: D 87 GLU cc_start: 0.8160 (tp30) cc_final: 0.7892 (mm-30) REVERT: D 89 GLN cc_start: 0.8941 (mm110) cc_final: 0.8709 (mm110) REVERT: D 103 HIS cc_start: 0.6750 (m-70) cc_final: 0.6517 (m-70) outliers start: 0 outliers final: 0 residues processed: 453 average time/residue: 0.1290 time to fit residues: 82.3024 Evaluate side-chains 426 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 426 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 53 optimal weight: 0.0270 chunk 95 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 320 HIS ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.156029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.121257 restraints weight = 30745.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125614 restraints weight = 17774.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.128612 restraints weight = 11729.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130771 restraints weight = 8361.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.132057 restraints weight = 6387.878| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3991 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= 0.144 Angle : 0.719 12.098 19562 Z= 0.374 Chirality : 0.043 0.170 2195 Planarity : 0.005 0.062 2244 Dihedral : 21.150 169.186 2554 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.14 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.17 (0.21), residues: 1535 helix: 0.12 (0.21), residues: 585 sheet: -0.50 (0.34), residues: 244 loop : -1.63 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 472 TYR 0.024 0.002 TYR A 595 PHE 0.076 0.002 PHE A 589 TRP 0.062 0.003 TRP A 259 HIS 0.009 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00308 (14204) covalent geometry : angle 0.71870 (19562) hydrogen bonds : bond 0.04186 ( 580) hydrogen bonds : angle 5.09440 ( 1605) Misc. bond : bond 0.00063 ( 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 450 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 0.495 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: 0.9101 (mttt) cc_final: 0.8859 (mttp) REVERT: A 65 ASP cc_start: 0.8595 (t70) cc_final: 0.8215 (t0) REVERT: A 66 PHE cc_start: 0.7257 (m-80) cc_final: 0.6906 (m-80) REVERT: A 226 VAL cc_start: 0.8857 (p) cc_final: 0.8494 (p) REVERT: A 228 ARG cc_start: 0.8141 (ttp-170) cc_final: 0.7672 (ttp-170) REVERT: A 231 LYS cc_start: 0.9040 (mptt) cc_final: 0.8730 (mptt) REVERT: A 255 LEU cc_start: 0.7742 (mt) cc_final: 0.7465 (mt) REVERT: A 260 ASP cc_start: 0.8003 (p0) cc_final: 0.7780 (p0) REVERT: A 293 LYS cc_start: 0.8017 (pttm) cc_final: 0.7396 (pttm) REVERT: A 305 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8206 (tp30) REVERT: A 316 MET cc_start: 0.7084 (tmm) cc_final: 0.6695 (tpp) REVERT: A 320 HIS cc_start: 0.7083 (t-90) cc_final: 0.6704 (t-170) REVERT: A 323 GLN cc_start: 0.8423 (tm-30) cc_final: 0.8175 (tm-30) REVERT: A 324 THR cc_start: 0.7976 (p) cc_final: 0.7607 (p) REVERT: A 328 LEU cc_start: 0.8198 (mt) cc_final: 0.7994 (mt) REVERT: A 346 GLU cc_start: 0.7866 (mp0) cc_final: 0.7565 (mp0) REVERT: A 351 LYS cc_start: 0.8415 (tttp) cc_final: 0.7532 (mmtm) REVERT: A 355 ARG cc_start: 0.8358 (ttm110) cc_final: 0.7615 (ttm110) REVERT: A 368 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8450 (mtpt) REVERT: A 370 LEU cc_start: 0.8978 (tt) cc_final: 0.8712 (tt) REVERT: A 379 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7394 (mtp85) REVERT: A 382 HIS cc_start: 0.7476 (t-90) cc_final: 0.7082 (t-90) REVERT: A 394 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8205 (ttpt) REVERT: A 409 TYR cc_start: 0.8680 (t80) cc_final: 0.8314 (t80) REVERT: A 426 TYR cc_start: 0.7073 (p90) cc_final: 0.6768 (p90) REVERT: A 456 MET cc_start: 0.8475 (mtm) cc_final: 0.7958 (mtm) REVERT: A 482 LYS cc_start: 0.7743 (mmmm) cc_final: 0.7086 (mmmm) REVERT: A 489 ASN cc_start: 0.6777 (p0) cc_final: 0.6548 (p0) REVERT: A 502 LEU cc_start: 0.9060 (pp) cc_final: 0.8559 (pp) REVERT: A 516 VAL cc_start: 0.8809 (m) cc_final: 0.8251 (p) REVERT: A 519 ASN cc_start: 0.7727 (m110) cc_final: 0.7485 (m110) REVERT: A 520 ASN cc_start: 0.8864 (m-40) cc_final: 0.8517 (m-40) REVERT: A 525 ASN cc_start: 0.6980 (m110) cc_final: 0.6480 (m110) REVERT: A 540 LEU cc_start: 0.7855 (tp) cc_final: 0.7421 (tt) REVERT: A 560 ILE cc_start: 0.8201 (mt) cc_final: 0.7922 (pt) REVERT: A 565 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 569 ASN cc_start: 0.7152 (m110) cc_final: 0.6821 (m110) REVERT: A 575 LYS cc_start: 0.8047 (mmtm) cc_final: 0.7805 (mmtm) REVERT: A 590 LYS cc_start: 0.8918 (mptt) cc_final: 0.8446 (mmmt) REVERT: B 136 LYS cc_start: 0.7812 (mmpt) cc_final: 0.7185 (mmpt) REVERT: C 30 LYS cc_start: 0.8082 (mttt) cc_final: 0.7856 (mttt) REVERT: C 32 LEU cc_start: 0.7889 (mt) cc_final: 0.7631 (mt) REVERT: C 41 TYR cc_start: 0.7150 (p90) cc_final: 0.6940 (p90) REVERT: C 53 LYS cc_start: 0.6725 (mppt) cc_final: 0.6123 (mppt) REVERT: C 84 GLN cc_start: 0.7985 (mp10) cc_final: 0.7112 (mp10) REVERT: C 90 LYS cc_start: 0.8549 (ptmm) cc_final: 0.7997 (ptmm) REVERT: C 95 LYS cc_start: 0.9132 (mppt) cc_final: 0.8672 (mppt) REVERT: C 98 MET cc_start: 0.7469 (ttm) cc_final: 0.7068 (ttm) REVERT: C 128 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7130 (mt-10) REVERT: C 139 LYS cc_start: 0.7701 (tmmt) cc_final: 0.7128 (pttp) REVERT: C 144 GLU cc_start: 0.7151 (tp30) cc_final: 0.6621 (tm-30) REVERT: C 159 ASP cc_start: 0.7455 (t0) cc_final: 0.6823 (t0) REVERT: C 164 MET cc_start: 0.8501 (ppp) cc_final: 0.8226 (ppp) REVERT: C 199 TYR cc_start: 0.7996 (t80) cc_final: 0.7521 (t80) REVERT: C 204 TYR cc_start: 0.7771 (m-80) cc_final: 0.7378 (m-10) REVERT: C 218 GLN cc_start: 0.7525 (mt0) cc_final: 0.7030 (mt0) REVERT: C 225 CYS cc_start: 0.8554 (m) cc_final: 0.8311 (m) REVERT: C 236 LYS cc_start: 0.8763 (mppt) cc_final: 0.8225 (mppt) REVERT: C 244 GLN cc_start: 0.6065 (tp-100) cc_final: 0.5721 (tp-100) REVERT: C 263 ARG cc_start: 0.8263 (ptt180) cc_final: 0.6957 (ptt180) REVERT: C 267 ARG cc_start: 0.8024 (ppt170) cc_final: 0.7629 (ppt170) REVERT: C 305 GLU cc_start: 0.8040 (tp30) cc_final: 0.7752 (tp30) REVERT: C 306 MET cc_start: 0.8080 (tmm) cc_final: 0.7423 (tmm) REVERT: C 308 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8075 (ttm-80) REVERT: C 316 MET cc_start: 0.7327 (mtt) cc_final: 0.7125 (mtt) REVERT: C 350 LEU cc_start: 0.8811 (mm) cc_final: 0.8588 (mm) REVERT: C 351 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8604 (mtpp) REVERT: C 365 ASP cc_start: 0.7838 (p0) cc_final: 0.7582 (p0) REVERT: C 367 VAL cc_start: 0.8943 (t) cc_final: 0.8641 (p) REVERT: C 409 TYR cc_start: 0.8518 (t80) cc_final: 0.7912 (t80) REVERT: C 410 GLU cc_start: 0.8316 (tt0) cc_final: 0.8037 (tt0) REVERT: C 476 PHE cc_start: 0.7943 (m-80) cc_final: 0.7699 (m-80) REVERT: C 504 GLU cc_start: 0.8385 (tp30) cc_final: 0.7884 (tp30) REVERT: C 518 ILE cc_start: 0.8853 (mm) cc_final: 0.8403 (mm) REVERT: C 522 CYS cc_start: 0.8729 (m) cc_final: 0.8502 (m) REVERT: C 536 LYS cc_start: 0.7864 (ttmt) cc_final: 0.7463 (ttmt) REVERT: C 549 TYR cc_start: 0.7571 (m-80) cc_final: 0.7289 (m-80) REVERT: C 550 LYS cc_start: 0.8379 (mttt) cc_final: 0.8169 (mttt) REVERT: C 557 LEU cc_start: 0.8978 (mm) cc_final: 0.8740 (mm) REVERT: C 566 LYS cc_start: 0.8726 (pttp) cc_final: 0.8307 (pttp) REVERT: C 584 HIS cc_start: 0.8509 (m90) cc_final: 0.8247 (m90) REVERT: C 590 LYS cc_start: 0.8477 (tttt) cc_final: 0.8033 (tttt) REVERT: C 603 MET cc_start: 0.7636 (mtt) cc_final: 0.7362 (mtt) REVERT: D 66 GLU cc_start: 0.8713 (mp0) cc_final: 0.8428 (mp0) REVERT: D 78 ASN cc_start: 0.8964 (t0) cc_final: 0.8571 (t0) REVERT: D 87 GLU cc_start: 0.8161 (tp30) cc_final: 0.7869 (mm-30) REVERT: D 89 GLN cc_start: 0.8932 (mm110) cc_final: 0.8703 (mm110) REVERT: D 93 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.8121 (tmm-80) REVERT: D 103 HIS cc_start: 0.6767 (m-70) cc_final: 0.6563 (m-70) REVERT: D 126 LYS cc_start: 0.8048 (tptp) cc_final: 0.7637 (tptp) outliers start: 0 outliers final: 0 residues processed: 450 average time/residue: 0.1245 time to fit residues: 78.8483 Evaluate side-chains 420 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 113 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 73 optimal weight: 0.2980 chunk 25 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 45 optimal weight: 0.1980 chunk 95 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.157208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.122172 restraints weight = 30257.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126556 restraints weight = 17712.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129528 restraints weight = 11654.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.131643 restraints weight = 8372.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.132996 restraints weight = 6440.188| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.4172 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= 0.142 Angle : 0.737 12.348 19562 Z= 0.379 Chirality : 0.043 0.172 2195 Planarity : 0.005 0.061 2244 Dihedral : 21.139 169.353 2554 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.53 % Favored : 91.34 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.21), residues: 1535 helix: 0.12 (0.21), residues: 582 sheet: -0.47 (0.35), residues: 233 loop : -1.58 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 46 TYR 0.028 0.002 TYR A 41 PHE 0.022 0.001 PHE A 589 TRP 0.026 0.002 TRP A 406 HIS 0.010 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00307 (14204) covalent geometry : angle 0.73673 (19562) hydrogen bonds : bond 0.04174 ( 580) hydrogen bonds : angle 5.05359 ( 1605) Misc. bond : bond 0.00062 ( 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 440 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7692 (tpt) cc_final: 0.7471 (tpt) REVERT: A 2 LYS cc_start: 0.9089 (mttt) cc_final: 0.8854 (mttp) REVERT: A 65 ASP cc_start: 0.8525 (t70) cc_final: 0.8240 (t0) REVERT: A 66 PHE cc_start: 0.7231 (m-80) cc_final: 0.6949 (m-80) REVERT: A 181 ARG cc_start: 0.8654 (ttp80) cc_final: 0.8240 (ttp80) REVERT: A 222 LEU cc_start: 0.8863 (tp) cc_final: 0.8656 (tp) REVERT: A 226 VAL cc_start: 0.8878 (p) cc_final: 0.8504 (p) REVERT: A 228 ARG cc_start: 0.8087 (ttp-170) cc_final: 0.7467 (ttp80) REVERT: A 231 LYS cc_start: 0.9035 (mptt) cc_final: 0.8725 (mptt) REVERT: A 246 LYS cc_start: 0.7694 (pttp) cc_final: 0.7371 (tmtt) REVERT: A 255 LEU cc_start: 0.7754 (mt) cc_final: 0.7276 (mt) REVERT: A 260 ASP cc_start: 0.7944 (p0) cc_final: 0.7728 (p0) REVERT: A 293 LYS cc_start: 0.7985 (pttm) cc_final: 0.7441 (pttm) REVERT: A 305 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8190 (tp30) REVERT: A 316 MET cc_start: 0.7096 (tmm) cc_final: 0.6733 (tpp) REVERT: A 320 HIS cc_start: 0.7102 (t-90) cc_final: 0.6672 (t-170) REVERT: A 323 GLN cc_start: 0.8426 (tm-30) cc_final: 0.8163 (tm-30) REVERT: A 324 THR cc_start: 0.8004 (p) cc_final: 0.7635 (p) REVERT: A 328 LEU cc_start: 0.8244 (mt) cc_final: 0.8019 (mt) REVERT: A 346 GLU cc_start: 0.7855 (mp0) cc_final: 0.7550 (mp0) REVERT: A 348 PHE cc_start: 0.8864 (t80) cc_final: 0.8568 (t80) REVERT: A 351 LYS cc_start: 0.8429 (tttp) cc_final: 0.7632 (ttmm) REVERT: A 355 ARG cc_start: 0.8383 (ttm110) cc_final: 0.7627 (ttm110) REVERT: A 368 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8441 (mtpt) REVERT: A 379 ARG cc_start: 0.7806 (mtp85) cc_final: 0.7424 (mtp85) REVERT: A 382 HIS cc_start: 0.7487 (t-90) cc_final: 0.7076 (t-90) REVERT: A 394 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8197 (ttpt) REVERT: A 398 GLU cc_start: 0.7310 (pm20) cc_final: 0.6997 (pm20) REVERT: A 409 TYR cc_start: 0.8672 (t80) cc_final: 0.8301 (t80) REVERT: A 482 LYS cc_start: 0.7676 (mmmm) cc_final: 0.7036 (mmmm) REVERT: A 489 ASN cc_start: 0.6662 (p0) cc_final: 0.6448 (p0) REVERT: A 501 THR cc_start: 0.8684 (p) cc_final: 0.8454 (p) REVERT: A 502 LEU cc_start: 0.9053 (pp) cc_final: 0.8542 (pp) REVERT: A 516 VAL cc_start: 0.8805 (m) cc_final: 0.8260 (p) REVERT: A 519 ASN cc_start: 0.7728 (m110) cc_final: 0.7465 (m110) REVERT: A 520 ASN cc_start: 0.8865 (m-40) cc_final: 0.8541 (m-40) REVERT: A 525 ASN cc_start: 0.6979 (m110) cc_final: 0.6515 (m110) REVERT: A 560 ILE cc_start: 0.8177 (mt) cc_final: 0.7888 (pt) REVERT: A 565 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7605 (mt-10) REVERT: A 569 ASN cc_start: 0.7178 (m110) cc_final: 0.6763 (m110) REVERT: A 585 THR cc_start: 0.7844 (t) cc_final: 0.7494 (t) REVERT: A 590 LYS cc_start: 0.8887 (mptt) cc_final: 0.8203 (mmmt) REVERT: A 594 HIS cc_start: 0.8291 (m90) cc_final: 0.7996 (m-70) REVERT: B 106 CYS cc_start: 0.7298 (t) cc_final: 0.6597 (m) REVERT: B 136 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7270 (mmpt) REVERT: C 30 LYS cc_start: 0.8102 (mttt) cc_final: 0.7878 (mttt) REVERT: C 32 LEU cc_start: 0.7901 (mt) cc_final: 0.7645 (mt) REVERT: C 53 LYS cc_start: 0.6699 (mppt) cc_final: 0.6114 (mppt) REVERT: C 84 GLN cc_start: 0.7957 (mp10) cc_final: 0.7080 (mp10) REVERT: C 95 LYS cc_start: 0.9130 (mppt) cc_final: 0.8682 (mppt) REVERT: C 139 LYS cc_start: 0.7696 (tmmt) cc_final: 0.7154 (pttp) REVERT: C 144 GLU cc_start: 0.7129 (tp30) cc_final: 0.6613 (tm-30) REVERT: C 159 ASP cc_start: 0.7467 (t0) cc_final: 0.6831 (t0) REVERT: C 164 MET cc_start: 0.8489 (ppp) cc_final: 0.8176 (ppp) REVERT: C 204 TYR cc_start: 0.7761 (m-80) cc_final: 0.7276 (m-10) REVERT: C 218 GLN cc_start: 0.7594 (mt0) cc_final: 0.7082 (mt0) REVERT: C 225 CYS cc_start: 0.8547 (m) cc_final: 0.8297 (m) REVERT: C 236 LYS cc_start: 0.8763 (mppt) cc_final: 0.8239 (mppt) REVERT: C 244 GLN cc_start: 0.6030 (tp-100) cc_final: 0.5722 (tp-100) REVERT: C 263 ARG cc_start: 0.8214 (ptt180) cc_final: 0.6957 (ptt180) REVERT: C 267 ARG cc_start: 0.8026 (ppt170) cc_final: 0.7647 (ppt170) REVERT: C 273 PHE cc_start: 0.8219 (m-10) cc_final: 0.7959 (m-10) REVERT: C 305 GLU cc_start: 0.8018 (tp30) cc_final: 0.7722 (tp30) REVERT: C 306 MET cc_start: 0.8052 (tmm) cc_final: 0.7409 (tmm) REVERT: C 308 ARG cc_start: 0.8537 (ttp-170) cc_final: 0.8042 (ttm-80) REVERT: C 316 MET cc_start: 0.7356 (mtt) cc_final: 0.7147 (mtt) REVERT: C 350 LEU cc_start: 0.8812 (mm) cc_final: 0.8599 (mm) REVERT: C 351 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8603 (mtpp) REVERT: C 365 ASP cc_start: 0.7852 (p0) cc_final: 0.7584 (p0) REVERT: C 409 TYR cc_start: 0.8519 (t80) cc_final: 0.7862 (t80) REVERT: C 410 GLU cc_start: 0.8321 (tt0) cc_final: 0.8015 (tt0) REVERT: C 445 LYS cc_start: 0.7860 (mttp) cc_final: 0.7613 (mttm) REVERT: C 504 GLU cc_start: 0.8326 (tp30) cc_final: 0.7860 (tp30) REVERT: C 518 ILE cc_start: 0.8829 (mm) cc_final: 0.8364 (mm) REVERT: C 520 ASN cc_start: 0.8248 (m110) cc_final: 0.7799 (m110) REVERT: C 522 CYS cc_start: 0.8672 (m) cc_final: 0.8467 (m) REVERT: C 536 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7472 (ttmt) REVERT: C 549 TYR cc_start: 0.7524 (m-80) cc_final: 0.7253 (m-80) REVERT: C 557 LEU cc_start: 0.8994 (mm) cc_final: 0.8786 (mm) REVERT: C 584 HIS cc_start: 0.8500 (m90) cc_final: 0.8234 (m90) REVERT: C 590 LYS cc_start: 0.8480 (tttt) cc_final: 0.7516 (tttt) REVERT: C 591 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7537 (mmm160) REVERT: C 603 MET cc_start: 0.7462 (mtt) cc_final: 0.7258 (mtt) REVERT: D 18 ASP cc_start: 0.6196 (m-30) cc_final: 0.5873 (m-30) REVERT: D 32 ASN cc_start: 0.8975 (t0) cc_final: 0.8766 (t0) REVERT: D 66 GLU cc_start: 0.8678 (mp0) cc_final: 0.8414 (mp0) REVERT: D 78 ASN cc_start: 0.8910 (t0) cc_final: 0.8502 (t0) REVERT: D 87 GLU cc_start: 0.8146 (tp30) cc_final: 0.7868 (mm-30) REVERT: D 89 GLN cc_start: 0.8925 (mm110) cc_final: 0.8692 (mm110) REVERT: D 93 ARG cc_start: 0.8359 (tmm-80) cc_final: 0.8112 (tmm-80) REVERT: D 126 LYS cc_start: 0.7966 (tptp) cc_final: 0.7657 (tptp) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.1309 time to fit residues: 80.9300 Evaluate side-chains 416 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 10 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 147 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 84 optimal weight: 0.0870 chunk 56 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 55 optimal weight: 0.0370 chunk 52 optimal weight: 0.0170 chunk 12 optimal weight: 6.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- 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** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.158439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.123346 restraints weight = 30449.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127749 restraints weight = 17725.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130784 restraints weight = 11673.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132930 restraints weight = 8357.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.134366 restraints weight = 6403.302| |-----------------------------------------------------------------------------| r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14205 Z= 0.138 Angle : 0.736 12.380 19562 Z= 0.380 Chirality : 0.043 0.179 2195 Planarity : 0.005 0.060 2244 Dihedral : 21.113 169.303 2554 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.75 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.11 (0.22), residues: 1535 helix: 0.15 (0.21), residues: 586 sheet: -0.47 (0.34), residues: 237 loop : -1.57 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 472 TYR 0.023 0.002 TYR A 595 PHE 0.028 0.001 PHE A 589 TRP 0.059 0.003 TRP A 259 HIS 0.012 0.001 HIS A 506 Details of bonding type rmsd covalent geometry : bond 0.00298 (14204) covalent geometry : angle 0.73572 (19562) hydrogen bonds : bond 0.04101 ( 580) hydrogen bonds : angle 4.99363 ( 1605) Misc. bond : bond 0.00055 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.07 seconds wall clock time: 47 minutes 20.67 seconds (2840.67 seconds total)