Starting phenix.real_space_refine on Thu Jun 12 09:23:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c9w_45374/06_2025/9c9w_45374_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c9w_45374/06_2025/9c9w_45374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c9w_45374/06_2025/9c9w_45374.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c9w_45374/06_2025/9c9w_45374.map" model { file = "/net/cci-nas-00/data/ceres_data/9c9w_45374/06_2025/9c9w_45374_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c9w_45374/06_2025/9c9w_45374_neut.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 80 5.49 5 S 78 5.16 5 C 8443 2.51 5 N 2385 2.21 5 O 2774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 13761 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4841 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Chain: "B" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "C" Number of atoms: 4845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4845 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 30, 'TRANS': 581} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1219 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 153} Chain: "E" Number of atoms: 475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 475 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 771 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.65, per 1000 atoms: 0.63 Number of scatterers: 13761 At special positions: 0 Unit cell: (92.96, 140.27, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 78 16.00 P 80 15.00 O 2774 8.00 N 2385 7.00 C 8443 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.7 seconds 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2884 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 11 sheets defined 42.4% alpha, 15.7% beta 25 base pairs and 51 stacking pairs defined. Time for finding SS restraints: 4.96 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: 4.82 Time building geometry restraints manager: 4.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3834 1.33 - 1.45: 2725 1.45 - 1.57: 7367 1.57 - 1.69: 155 1.69 - 1.81: 123 Bond restraints: 14204 Sorted by residual: bond pdb=" C SER C 335 " pdb=" N PTR C 336 " ideal model delta sigma weight residual 1.329 1.430 -0.101 1.40e-02 5.10e+03 5.21e+01 bond pdb=" N GLN A 331 " pdb=" CA GLN A 331 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.35e-02 5.49e+03 1.18e+01 bond pdb=" N HIS A 387 " pdb=" CA HIS A 387 " ideal model delta sigma weight residual 1.456 1.485 -0.029 9.80e-03 1.04e+04 8.61e+00 bond pdb=" C LEU A 328 " pdb=" O LEU A 328 " ideal model delta sigma weight residual 1.237 1.266 -0.030 1.16e-02 7.43e+03 6.62e+00 bond pdb=" N SER A 289 " pdb=" CA SER A 289 " ideal model delta sigma weight residual 1.454 1.483 -0.029 1.27e-02 6.20e+03 5.24e+00 ... (remaining 14199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.75: 19536 5.75 - 11.51: 21 11.51 - 17.26: 3 17.26 - 23.01: 1 23.01 - 28.76: 1 Bond angle restraints: 19562 Sorted by residual: angle pdb=" O SER C 335 " pdb=" C SER C 335 " pdb=" N PTR C 336 " ideal model delta sigma weight residual 123.00 94.24 28.76 1.60e+00 3.91e-01 3.23e+02 angle pdb=" N GLN A 331 " pdb=" CA GLN A 331 " pdb=" C GLN A 331 " ideal model delta sigma weight residual 113.01 97.68 15.33 1.20e+00 6.94e-01 1.63e+02 angle pdb=" CA SER C 335 " pdb=" C SER C 335 " pdb=" N PTR C 336 " ideal model delta sigma weight residual 116.20 136.10 -19.90 2.00e+00 2.50e-01 9.90e+01 angle pdb=" C SER C 335 " pdb=" N PTR C 336 " pdb=" CA PTR C 336 " ideal model delta sigma weight residual 121.70 137.34 -15.64 1.80e+00 3.09e-01 7.55e+01 angle pdb=" CA GLN A 331 " pdb=" C GLN A 331 " pdb=" N GLY A 332 " ideal model delta sigma weight residual 118.43 110.86 7.57 1.33e+00 5.65e-01 3.24e+01 ... (remaining 19557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.78: 7878 33.78 - 67.55: 503 67.55 - 101.33: 30 101.33 - 135.10: 0 135.10 - 168.88: 1 Dihedral angle restraints: 8412 sinusoidal: 3943 harmonic: 4469 Sorted by residual: dihedral pdb=" CA SER C 335 " pdb=" C SER C 335 " pdb=" N PTR C 336 " pdb=" CA PTR C 336 " ideal model delta harmonic sigma weight residual 180.00 -145.84 -34.16 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA PRO A 491 " pdb=" C PRO A 491 " pdb=" N ASP A 492 " pdb=" CA ASP A 492 " ideal model delta harmonic sigma weight residual 180.00 148.58 31.42 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA ASN A 489 " pdb=" C ASN A 489 " pdb=" N PRO A 490 " pdb=" CA PRO A 490 " ideal model delta harmonic sigma weight residual 180.00 155.56 24.44 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 8409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1686 0.045 - 0.091: 376 0.091 - 0.136: 115 0.136 - 0.182: 15 0.182 - 0.227: 3 Chirality restraints: 2195 Sorted by residual: chirality pdb=" CA GLN A 331 " pdb=" N GLN A 331 " pdb=" C GLN A 331 " pdb=" CB GLN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA PHE A 195 " pdb=" N PHE A 195 " pdb=" C PHE A 195 " pdb=" CB PHE A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 25 " pdb=" CA THR B 25 " pdb=" OG1 THR B 25 " pdb=" CG2 THR B 25 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 2192 not shown) Planarity restraints: 2244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER C 335 " 0.066 2.00e-02 2.50e+03 1.04e-01 1.07e+02 pdb=" C SER C 335 " -0.179 2.00e-02 2.50e+03 pdb=" O SER C 335 " 0.053 2.00e-02 2.50e+03 pdb=" N PTR C 336 " 0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 490 " -0.051 5.00e-02 4.00e+02 7.75e-02 9.62e+00 pdb=" N PRO A 491 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG L 42 " -0.014 2.00e-02 2.50e+03 1.62e-02 7.92e+00 pdb=" N9 DG L 42 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG L 42 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG L 42 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DG L 42 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG L 42 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG L 42 " -0.001 2.00e-02 2.50e+03 pdb=" N1 DG L 42 " -0.008 2.00e-02 2.50e+03 pdb=" C2 DG L 42 " 0.042 2.00e-02 2.50e+03 pdb=" N2 DG L 42 " -0.027 2.00e-02 2.50e+03 pdb=" N3 DG L 42 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG L 42 " -0.001 2.00e-02 2.50e+03 ... (remaining 2241 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 266 2.64 - 3.20: 13015 3.20 - 3.77: 22012 3.77 - 4.33: 28704 4.33 - 4.90: 43519 Nonbonded interactions: 107516 Sorted by model distance: nonbonded pdb=" O PRO D 122 " pdb=" OG1 THR D 125 " model vdw 2.070 3.040 nonbonded pdb=" O3' DA E 24 " pdb="MN MN E 101 " model vdw 2.112 2.320 nonbonded pdb=" NH1 ARG C 149 " pdb=" O ALA C 150 " model vdw 2.143 3.120 nonbonded pdb=" O SER D 118 " pdb=" OG1 THR D 121 " model vdw 2.158 3.040 nonbonded pdb=" O VAL A 309 " pdb=" O SER A 312 " model vdw 2.164 3.040 ... (remaining 107511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 335 or resid 337 through 611)) selection = (chain 'C' and (resid 0 through 335 or resid 337 through 611)) } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.560 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 37.130 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.476 14205 Z= 0.444 Angle : 0.802 28.764 19562 Z= 0.449 Chirality : 0.044 0.227 2195 Planarity : 0.005 0.104 2244 Dihedral : 19.220 168.878 5528 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.58 % Favored : 90.23 % Rotamer: Outliers : 0.15 % Allowed : 1.12 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.21), residues: 1535 helix: -0.20 (0.21), residues: 581 sheet: -0.83 (0.35), residues: 224 loop : -1.75 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 363 HIS 0.005 0.001 HIS C 39 PHE 0.041 0.002 PHE A 589 TYR 0.026 0.002 TYR A 595 ARG 0.010 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.16309 ( 580) hydrogen bonds : angle 6.96821 ( 1605) covalent geometry : bond 0.00356 (14204) covalent geometry : angle 0.80187 (19562) Misc. bond : bond 0.47641 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 469 time to evaluate : 1.270 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: 0.3152 time to fit residues: 200.4927 Evaluate side-chains 410 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 125 optimal weight: 0.0170 chunk 48 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN A 519 ASN A 523 GLN B 146 ASN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 360 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.158518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.124651 restraints weight = 29881.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.129072 restraints weight = 17185.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.132012 restraints weight = 11174.967| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14205 Z= 0.149 Angle : 0.682 9.665 19562 Z= 0.361 Chirality : 0.042 0.206 2195 Planarity : 0.005 0.053 2244 Dihedral : 21.057 168.813 2554 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.79 % Favored : 91.14 % Rotamer: Outliers : 0.45 % Allowed : 5.39 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1535 helix: -0.09 (0.21), residues: 589 sheet: -0.48 (0.36), residues: 230 loop : -1.72 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 406 HIS 0.008 0.001 HIS C 60 PHE 0.027 0.001 PHE A 589 TYR 0.024 0.002 TYR A 595 ARG 0.007 0.001 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.04802 ( 580) hydrogen bonds : angle 5.51818 ( 1605) covalent geometry : bond 0.00316 (14204) covalent geometry : angle 0.68232 (19562) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 451 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9090 (mttt) cc_final: 0.8853 (mttp) REVERT: A 66 PHE cc_start: 0.7302 (m-80) cc_final: 0.7030 (m-80) REVERT: A 218 GLN cc_start: 0.8574 (mm110) cc_final: 0.8200 (mm110) REVERT: A 226 VAL cc_start: 0.8696 (p) cc_final: 0.8486 (p) REVERT: A 231 LYS cc_start: 0.8926 (mptt) cc_final: 0.8632 (mptt) REVERT: A 232 ILE cc_start: 0.8973 (mt) cc_final: 0.8763 (mt) REVERT: A 233 GLN cc_start: 0.8744 (mm110) cc_final: 0.8289 (mp10) REVERT: A 244 GLN cc_start: 0.8509 (tp40) cc_final: 0.8131 (tp-100) REVERT: A 255 LEU cc_start: 0.7753 (mt) cc_final: 0.7362 (mm) REVERT: A 260 ASP cc_start: 0.7627 (p0) cc_final: 0.7366 (p0) REVERT: A 271 GLN cc_start: 0.8465 (tp-100) cc_final: 0.8092 (tp-100) REVERT: A 272 MET cc_start: 0.7231 (mtt) cc_final: 0.6521 (mtt) REVERT: A 293 LYS cc_start: 0.7919 (pttm) cc_final: 0.7293 (pttm) REVERT: A 303 THR cc_start: 0.8168 (m) cc_final: 0.7871 (p) REVERT: A 305 GLU cc_start: 0.8614 (tt0) cc_final: 0.7854 (tp30) REVERT: A 323 GLN cc_start: 0.8335 (tm-30) cc_final: 0.8106 (tm-30) REVERT: A 327 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8197 (tpp80) REVERT: A 346 GLU cc_start: 0.7625 (mp0) cc_final: 0.7322 (mp0) REVERT: A 351 LYS cc_start: 0.8593 (tttp) cc_final: 0.8252 (tppt) REVERT: A 355 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7812 (tpm170) REVERT: A 360 HIS cc_start: 0.8070 (t-90) cc_final: 0.7700 (t-90) REVERT: A 368 LYS cc_start: 0.8832 (mtpt) cc_final: 0.8461 (mtpt) REVERT: A 370 LEU cc_start: 0.8850 (tt) cc_final: 0.8641 (tt) REVERT: A 376 ASN cc_start: 0.7550 (p0) cc_final: 0.7344 (p0) REVERT: A 380 LYS cc_start: 0.8255 (ttpt) cc_final: 0.7987 (ttmt) REVERT: A 406 TRP cc_start: 0.8826 (t60) cc_final: 0.8505 (t60) REVERT: A 408 LEU cc_start: 0.8703 (tp) cc_final: 0.8202 (tp) REVERT: A 409 TYR cc_start: 0.8570 (t80) cc_final: 0.8281 (t80) REVERT: A 426 TYR cc_start: 0.6970 (p90) cc_final: 0.6603 (p90) REVERT: A 476 PHE cc_start: 0.7628 (m-80) cc_final: 0.7410 (m-80) REVERT: A 489 ASN cc_start: 0.7065 (p0) cc_final: 0.6742 (p0) REVERT: A 516 VAL cc_start: 0.8849 (m) cc_final: 0.8190 (p) REVERT: A 520 ASN cc_start: 0.8569 (m-40) cc_final: 0.8174 (m-40) REVERT: A 525 ASN cc_start: 0.6814 (m-40) cc_final: 0.6191 (m110) REVERT: A 565 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7722 (mt-10) REVERT: A 603 MET cc_start: 0.8514 (mtm) cc_final: 0.8296 (mtm) REVERT: C 1 MET cc_start: 0.5588 (pmm) cc_final: 0.5304 (pmm) REVERT: C 6 MET cc_start: 0.7403 (ptm) cc_final: 0.7168 (ptm) REVERT: C 48 GLN cc_start: 0.7332 (mp10) cc_final: 0.7088 (mp10) REVERT: C 51 ARG cc_start: 0.6541 (ttp-110) cc_final: 0.6331 (ttp-110) REVERT: C 53 LYS cc_start: 0.7677 (mppt) cc_final: 0.6842 (mppt) REVERT: C 66 PHE cc_start: 0.7112 (m-80) cc_final: 0.6874 (m-80) REVERT: C 95 LYS cc_start: 0.9053 (mppt) cc_final: 0.8484 (mppt) REVERT: C 128 GLU cc_start: 0.7601 (mt-10) cc_final: 0.6998 (mt-10) REVERT: C 139 LYS cc_start: 0.7278 (tmmt) cc_final: 0.6952 (tttm) REVERT: C 199 TYR cc_start: 0.8020 (t80) cc_final: 0.7702 (t80) REVERT: C 204 TYR cc_start: 0.7561 (m-80) cc_final: 0.7257 (m-10) REVERT: C 232 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7446 (mp) REVERT: C 236 LYS cc_start: 0.8643 (mppt) cc_final: 0.8033 (mppt) REVERT: C 244 GLN cc_start: 0.5948 (tp-100) cc_final: 0.5737 (tp-100) REVERT: C 262 VAL cc_start: 0.8869 (m) cc_final: 0.8655 (p) REVERT: C 301 LEU cc_start: 0.8404 (tp) cc_final: 0.8165 (tp) REVERT: C 302 ASN cc_start: 0.8354 (t0) cc_final: 0.8030 (m-40) REVERT: C 306 MET cc_start: 0.7926 (tmm) cc_final: 0.7416 (tmm) REVERT: C 308 ARG cc_start: 0.8713 (ttp-170) cc_final: 0.7921 (ttm-80) REVERT: C 351 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8093 (mtpp) REVERT: C 356 GLN cc_start: 0.8774 (mt0) cc_final: 0.8467 (mt0) REVERT: C 357 GLN cc_start: 0.7907 (tt0) cc_final: 0.7271 (tt0) REVERT: C 365 ASP cc_start: 0.8164 (p0) cc_final: 0.7819 (p0) REVERT: C 368 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8703 (ttmm) REVERT: C 398 GLU cc_start: 0.7764 (tt0) cc_final: 0.6868 (tt0) REVERT: C 415 HIS cc_start: 0.8070 (t-90) cc_final: 0.7771 (t-90) REVERT: C 438 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7493 (tp30) REVERT: C 442 CYS cc_start: 0.6440 (p) cc_final: 0.5875 (m) REVERT: C 476 PHE cc_start: 0.7927 (m-80) cc_final: 0.7640 (m-80) REVERT: C 500 ILE cc_start: 0.9088 (mm) cc_final: 0.8445 (mm) REVERT: C 503 MET cc_start: 0.8319 (tpp) cc_final: 0.8022 (tpp) REVERT: C 504 GLU cc_start: 0.8591 (tp30) cc_final: 0.8124 (tp30) REVERT: C 557 LEU cc_start: 0.8801 (mm) cc_final: 0.8481 (mm) REVERT: C 566 LYS cc_start: 0.8621 (pttp) cc_final: 0.8201 (pttp) REVERT: C 584 HIS cc_start: 0.8472 (m90) cc_final: 0.8120 (m90) REVERT: C 590 LYS cc_start: 0.8448 (tttt) cc_final: 0.8105 (tttt) REVERT: C 606 LEU cc_start: 0.8683 (mp) cc_final: 0.8436 (mp) REVERT: D 18 ASP cc_start: 0.6144 (m-30) cc_final: 0.5861 (m-30) REVERT: D 78 ASN cc_start: 0.8868 (t0) cc_final: 0.8262 (t0) REVERT: D 99 MET cc_start: 0.6983 (ttm) cc_final: 0.6368 (ttm) REVERT: D 103 HIS cc_start: 0.6314 (m-70) cc_final: 0.5985 (m90) REVERT: D 140 LEU cc_start: 0.8993 (tt) cc_final: 0.8793 (tt) outliers start: 6 outliers final: 1 residues processed: 453 average time/residue: 0.2973 time to fit residues: 185.1421 Evaluate side-chains 399 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 397 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 128 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 154 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 319 GLN C 387 HIS ** C 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 573 GLN D 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.156229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.121970 restraints weight = 29976.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.126318 restraints weight = 17314.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129235 restraints weight = 11308.344| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14205 Z= 0.161 Angle : 0.680 13.183 19562 Z= 0.361 Chirality : 0.042 0.179 2195 Planarity : 0.005 0.053 2244 Dihedral : 21.088 169.358 2554 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.79 % Favored : 91.14 % Rotamer: Outliers : 0.37 % Allowed : 5.39 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.21), residues: 1535 helix: -0.01 (0.21), residues: 587 sheet: -0.56 (0.35), residues: 240 loop : -1.68 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 363 HIS 0.006 0.001 HIS C 60 PHE 0.019 0.001 PHE A 589 TYR 0.024 0.002 TYR A 41 ARG 0.007 0.001 ARG C 407 Details of bonding type rmsd hydrogen bonds : bond 0.04594 ( 580) hydrogen bonds : angle 5.21747 ( 1605) covalent geometry : bond 0.00343 (14204) covalent geometry : angle 0.68043 (19562) Misc. bond : bond 0.00096 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3070 Ramachandran restraints generated. 1535 Oldfield, 0 Emsley, 1535 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 436 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9110 (mttt) cc_final: 0.8727 (mttp) REVERT: A 66 PHE cc_start: 0.7306 (m-80) cc_final: 0.6973 (m-80) REVERT: A 119 ASP cc_start: 0.8646 (p0) cc_final: 0.8429 (p0) REVERT: A 157 ASP cc_start: 0.9077 (m-30) cc_final: 0.8357 (t0) REVERT: A 181 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8300 (ttp80) REVERT: A 226 VAL cc_start: 0.8751 (p) cc_final: 0.8408 (p) REVERT: A 231 LYS cc_start: 0.8998 (mptt) cc_final: 0.8722 (mptt) REVERT: A 236 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8551 (tppt) REVERT: A 246 LYS cc_start: 0.7408 (tmtt) cc_final: 0.7156 (tptp) REVERT: A 255 LEU cc_start: 0.7764 (mt) cc_final: 0.7316 (mm) REVERT: A 260 ASP cc_start: 0.7731 (p0) cc_final: 0.7487 (p0) REVERT: A 290 ARG cc_start: 0.8398 (ppt170) cc_final: 0.7806 (ppt170) REVERT: A 293 LYS cc_start: 0.7986 (pttm) cc_final: 0.7315 (pttm) REVERT: A 305 GLU cc_start: 0.8641 (tt0) cc_final: 0.7956 (tp30) REVERT: A 316 MET cc_start: 0.7087 (tmm) cc_final: 0.6751 (tmm) REVERT: A 320 HIS cc_start: 0.7219 (t-90) cc_final: 0.6417 (t-90) REVERT: A 323 GLN cc_start: 0.8378 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 324 THR cc_start: 0.8162 (t) cc_final: 0.7901 (t) REVERT: A 346 GLU cc_start: 0.7792 (mp0) cc_final: 0.7435 (mp0) REVERT: A 351 LYS cc_start: 0.8608 (tttp) cc_final: 0.8241 (mmtm) REVERT: A 355 ARG cc_start: 0.8430 (tpm170) cc_final: 0.7774 (tpm170) REVERT: A 368 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8444 (mtpt) REVERT: A 369 ARG cc_start: 0.9096 (ptm-80) cc_final: 0.8688 (ptm-80) REVERT: A 370 LEU cc_start: 0.8872 (tt) cc_final: 0.8386 (tt) REVERT: A 380 LYS cc_start: 0.8283 (ttpt) cc_final: 0.8047 (ttmt) REVERT: A 406 TRP cc_start: 0.8838 (t60) cc_final: 0.8459 (t60) REVERT: A 409 TYR cc_start: 0.8686 (t80) cc_final: 0.8236 (t80) REVERT: A 426 TYR cc_start: 0.7077 (p90) cc_final: 0.6639 (p90) REVERT: A 489 ASN cc_start: 0.7194 (p0) cc_final: 0.6887 (p0) REVERT: A 505 LYS cc_start: 0.9229 (tmtt) cc_final: 0.8843 (tmtt) REVERT: A 516 VAL cc_start: 0.8887 (m) cc_final: 0.8229 (p) REVERT: A 520 ASN cc_start: 0.8693 (m-40) cc_final: 0.8346 (m-40) REVERT: A 525 ASN cc_start: 0.6868 (m-40) cc_final: 0.6243 (m110) REVERT: A 565 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 603 MET cc_start: 0.8525 (mtm) cc_final: 0.8238 (mtm) REVERT: B 136 LYS cc_start: 0.7655 (mmpt) cc_final: 0.7037 (mmpt) REVERT: C 15 GLN cc_start: 0.8350 (pp30) cc_final: 0.8086 (pp30) REVERT: C 30 LYS cc_start: 0.8035 (mttt) cc_final: 0.7835 (mttt) REVERT: C 53 LYS cc_start: 0.7575 (mppt) cc_final: 0.6746 (mppt) REVERT: C 64 LEU cc_start: 0.7729 (tt) cc_final: 0.7446 (tt) REVERT: C 71 ASN cc_start: 0.7608 (m110) cc_final: 0.7347 (m110) REVERT: C 89 LYS cc_start: 0.8318 (mmtm) cc_final: 0.7932 (mmtm) REVERT: C 95 LYS cc_start: 0.9099 (mppt) cc_final: 0.8593 (mppt) REVERT: C 128 GLU cc_start: 0.7546 (mt-10) cc_final: 0.6941 (mt-10) REVERT: C 137 MET cc_start: 0.7396 (pmm) cc_final: 0.7149 (ptp) REVERT: C 139 LYS cc_start: 0.7439 (tmmt) cc_final: 0.6937 (ptmm) REVERT: C 144 GLU cc_start: 0.7058 (tp30) cc_final: 0.6692 (tp30) REVERT: C 164 MET cc_start: 0.8632 (ppp) cc_final: 0.8412 (ppp) REVERT: C 199 TYR cc_start: 0.7980 (t80) cc_final: 0.7649 (t80) REVERT: C 204 TYR cc_start: 0.7698 (m-80) cc_final: 0.7383 (m-10) REVERT: C 232 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7653 (mp) REVERT: C 236 LYS cc_start: 0.8672 (mppt) cc_final: 0.8067 (mppt) REVERT: C 244 GLN cc_start: 0.5982 (tp-100) cc_final: 0.5750 (tp40) REVERT: C 262 VAL cc_start: 0.8857 (m) cc_final: 0.8628 (p) REVERT: C 267 ARG cc_start: 0.7831 (ptm-80) cc_final: 0.7537 (ptm-80) REVERT: C 292 GLU cc_start: 0.8622 (pm20) cc_final: 0.8422 (pm20) REVERT: C 301 LEU cc_start: 0.8453 (tp) cc_final: 0.8061 (tp) REVERT: C 302 ASN cc_start: 0.8334 (t0) cc_final: 0.7984 (m-40) REVERT: C 308 ARG cc_start: 0.8669 (ttp-170) cc_final: 0.8411 (ttp-170) REVERT: C 323 GLN cc_start: 0.8754 (mt0) cc_final: 0.8449 (mm-40) REVERT: C 351 LYS cc_start: 0.9018 (ttmm) cc_final: 0.8753 (tttm) REVERT: C 365 ASP cc_start: 0.8004 (p0) cc_final: 0.7679 (p0) REVERT: C 368 LYS cc_start: 0.9091 (ttmm) cc_final: 0.8866 (ttmm) REVERT: C 369 ARG cc_start: 0.8439 (mmp-170) cc_final: 0.8209 (mmp-170) REVERT: C 398 GLU cc_start: 0.8054 (tt0) cc_final: 0.7323 (tt0) REVERT: C 415 HIS cc_start: 0.7969 (t-90) cc_final: 0.7601 (t-90) REVERT: C 438 GLU cc_start: 0.8020 (mm-30) cc_final: 0.6768 (tp30) REVERT: C 442 CYS cc_start: 0.6615 (p) cc_final: 0.6106 (m) REVERT: C 476 PHE cc_start: 0.7958 (m-80) cc_final: 0.7643 (m-80) REVERT: C 503 MET cc_start: 0.8306 (tpp) cc_final: 0.7977 (tpp) REVERT: C 504 GLU cc_start: 0.8579 (tp30) cc_final: 0.8126 (tp30) REVERT: C 550 LYS cc_start: 0.8330 (mttt) cc_final: 0.8062 (mttt) REVERT: C 557 LEU cc_start: 0.8845 (mm) cc_final: 0.8490 (mm) REVERT: C 566 LYS cc_start: 0.8691 (pttp) cc_final: 0.8312 (pttp) REVERT: C 584 HIS cc_start: 0.8483 (m90) cc_final: 0.8152 (m90) REVERT: C 590 LYS cc_start: 0.8513 (tttt) cc_final: 0.8215 (tttt) REVERT: C 603 MET cc_start: 0.7630 (mtt) cc_final: 0.7397 (mtt) REVERT: C 606 LEU cc_start: 0.8692 (mp) cc_final: 0.8405 (mp) REVERT: D 78 ASN cc_start: 0.8992 (t0) cc_final: 0.8500 (t0) REVERT: D 99 MET cc_start: 0.7002 (ttm) cc_final: 0.6740 (ttm) REVERT: D 103 HIS cc_start: 0.6498 (m-70) cc_final: 0.6202 (m90) REVERT: D 114 MET cc_start: 0.8195 (tmm) cc_final: 0.7030 (tmm) REVERT: D 140 LEU cc_start: 0.8996 (tt) cc_final: 0.8764 (tt) REVERT: D 159 GLU cc_start: 0.8357 (mp0) cc_final: 0.8109 (mp0) outliers start: 5 outliers final: 1 residues processed: 437 average time/residue: 0.2924 time to fit residues: 176.2725 Evaluate side-chains 399 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 397 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 93 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 20 optimal weight: 0.0000 chunk 140 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.0030 chunk 63 optimal weight: 0.0870 chunk 95 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 overall best weight: 0.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 319 GLN C 356 GLN C 387 HIS ** 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 = 0.4149 r_free = 0.4149 target = 0.157551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.123395 restraints weight = 29818.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.127793 restraints weight = 17137.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.130798 restraints weight = 11167.995| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14205 Z= 0.134 Angle : 0.672 9.889 19562 Z= 0.353 Chirality : 0.042 0.170 2195 Planarity : 0.004 0.055 2244 Dihedral : 21.075 168.837 2554 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.01 % Favored : 91.92 % Rotamer: Outliers : 0.37 % Allowed : 3.37 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.21), residues: 1535 helix: 0.09 (0.21), residues: 588 sheet: -0.37 (0.36), residues: 224 loop : -1.70 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 241 HIS 0.008 0.001 HIS C 60 PHE 0.039 0.001 PHE A 589 TYR 0.028 0.002 TYR A 41 ARG 0.008 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04313 ( 580) hydrogen bonds : angle 5.10746 ( 1605) covalent geometry : bond 0.00287 (14204) covalent geometry : angle 0.67170 (19562) Misc. bond : bond 0.00107 ( 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 459 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 454 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9111 (mttt) cc_final: 0.8850 (mttp) REVERT: A 65 ASP cc_start: 0.8595 (t70) cc_final: 0.8224 (t0) REVERT: A 66 PHE cc_start: 0.7330 (m-80) cc_final: 0.6996 (m-80) REVERT: A 119 ASP cc_start: 0.8662 (p0) cc_final: 0.8412 (p0) REVERT: A 157 ASP cc_start: 0.8999 (m-30) cc_final: 0.8301 (p0) REVERT: A 160 ILE cc_start: 0.8032 (pt) cc_final: 0.7707 (pt) REVERT: A 164 MET cc_start: 0.9118 (ptp) cc_final: 0.8870 (ptp) REVERT: A 231 LYS cc_start: 0.8950 (mptt) cc_final: 0.8670 (mptt) REVERT: A 255 LEU cc_start: 0.7751 (mt) cc_final: 0.7339 (mm) REVERT: A 260 ASP cc_start: 0.7694 (p0) cc_final: 0.7380 (p0) REVERT: A 290 ARG cc_start: 0.8395 (ppt170) cc_final: 0.7811 (ppt170) REVERT: A 293 LYS cc_start: 0.7940 (pttm) cc_final: 0.7297 (pttm) REVERT: A 303 THR cc_start: 0.8194 (m) cc_final: 0.7950 (p) REVERT: A 305 GLU cc_start: 0.8647 (tt0) cc_final: 0.7913 (tp30) REVERT: A 320 HIS cc_start: 0.7228 (t-90) cc_final: 0.6853 (t-90) REVERT: A 324 THR cc_start: 0.8097 (t) cc_final: 0.7872 (t) REVERT: A 346 GLU cc_start: 0.7807 (mp0) cc_final: 0.7466 (mp0) REVERT: A 348 PHE cc_start: 0.8763 (t80) cc_final: 0.8480 (t80) REVERT: A 351 LYS cc_start: 0.8663 (tttp) cc_final: 0.7643 (mmtm) REVERT: A 368 LYS cc_start: 0.8844 (mtpt) cc_final: 0.8498 (mtpt) REVERT: A 369 ARG cc_start: 0.9084 (ptm-80) cc_final: 0.8685 (ptm-80) REVERT: A 370 LEU cc_start: 0.8879 (tt) cc_final: 0.8436 (tt) REVERT: A 380 LYS cc_start: 0.8287 (ttpt) cc_final: 0.8057 (ttmt) REVERT: A 406 TRP cc_start: 0.8821 (t60) cc_final: 0.8279 (t60) REVERT: A 409 TYR cc_start: 0.8645 (t80) cc_final: 0.8251 (t80) REVERT: A 426 TYR cc_start: 0.7012 (p90) cc_final: 0.6649 (p90) REVERT: A 489 ASN cc_start: 0.7035 (p0) cc_final: 0.6729 (p0) REVERT: A 505 LYS cc_start: 0.9219 (tmtt) cc_final: 0.8828 (tmtt) REVERT: A 516 VAL cc_start: 0.8822 (m) cc_final: 0.8210 (p) REVERT: A 520 ASN cc_start: 0.8731 (m-40) cc_final: 0.8353 (m-40) REVERT: A 525 ASN cc_start: 0.6757 (m-40) cc_final: 0.6157 (m110) REVERT: A 560 ILE cc_start: 0.8044 (mt) cc_final: 0.7772 (pt) REVERT: A 565 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7558 (mt-10) REVERT: A 569 ASN cc_start: 0.6923 (m110) cc_final: 0.6674 (m110) REVERT: A 603 MET cc_start: 0.8463 (mtm) cc_final: 0.8259 (mtm) REVERT: B 37 ILE cc_start: 0.8812 (pt) cc_final: 0.8607 (pt) REVERT: B 136 LYS cc_start: 0.7857 (mmpt) cc_final: 0.7402 (mmpt) REVERT: C 30 LYS cc_start: 0.8045 (mttt) cc_final: 0.7822 (mttt) REVERT: C 32 LEU cc_start: 0.7903 (mt) cc_final: 0.7698 (mt) REVERT: C 53 LYS cc_start: 0.7429 (mppt) cc_final: 0.6675 (tppt) REVERT: C 71 ASN cc_start: 0.7637 (m110) cc_final: 0.7373 (m110) REVERT: C 89 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7922 (mmtm) REVERT: C 95 LYS cc_start: 0.9117 (mppt) cc_final: 0.8652 (mppt) REVERT: C 128 GLU cc_start: 0.7598 (mt-10) cc_final: 0.7003 (mt-10) REVERT: C 139 LYS cc_start: 0.7452 (tmmt) cc_final: 0.7014 (ptmm) REVERT: C 144 GLU cc_start: 0.7014 (tp30) cc_final: 0.6641 (tp30) REVERT: C 164 MET cc_start: 0.8592 (ppp) cc_final: 0.8190 (ppp) REVERT: C 199 TYR cc_start: 0.7881 (t80) cc_final: 0.7622 (t80) REVERT: C 204 TYR cc_start: 0.7633 (m-80) cc_final: 0.7295 (m-10) REVERT: C 232 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7593 (mp) REVERT: C 236 LYS cc_start: 0.8671 (mppt) cc_final: 0.8078 (mppt) REVERT: C 244 GLN cc_start: 0.5955 (tp-100) cc_final: 0.5699 (tp40) REVERT: C 262 VAL cc_start: 0.8866 (m) cc_final: 0.8605 (p) REVERT: C 263 ARG cc_start: 0.8267 (ptt180) cc_final: 0.6836 (ptt180) REVERT: C 302 ASN cc_start: 0.8345 (t0) cc_final: 0.7925 (m-40) REVERT: C 306 MET cc_start: 0.8032 (tmm) cc_final: 0.7419 (tmm) REVERT: C 308 ARG cc_start: 0.8642 (ttp-170) cc_final: 0.8200 (ttm-80) REVERT: C 323 GLN cc_start: 0.8731 (mt0) cc_final: 0.8428 (mm-40) REVERT: C 351 LYS cc_start: 0.9044 (ttmm) cc_final: 0.8655 (mtpp) REVERT: C 357 GLN cc_start: 0.8067 (tt0) cc_final: 0.7231 (tt0) REVERT: C 365 ASP cc_start: 0.7953 (p0) cc_final: 0.7651 (p0) REVERT: C 398 GLU cc_start: 0.8043 (tt0) cc_final: 0.7299 (tt0) REVERT: C 438 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7024 (tp30) REVERT: C 442 CYS cc_start: 0.6562 (p) cc_final: 0.6089 (m) REVERT: C 449 SER cc_start: 0.8665 (t) cc_final: 0.8463 (t) REVERT: C 464 GLU cc_start: 0.7097 (mp0) cc_final: 0.6877 (mp0) REVERT: C 476 PHE cc_start: 0.7941 (m-80) cc_final: 0.7666 (m-80) REVERT: C 504 GLU cc_start: 0.8562 (tp30) cc_final: 0.8131 (tp30) REVERT: C 550 LYS cc_start: 0.8341 (mttt) cc_final: 0.8087 (mttt) REVERT: C 557 LEU cc_start: 0.8861 (mm) cc_final: 0.8530 (mm) REVERT: C 566 LYS cc_start: 0.8663 (pttp) cc_final: 0.8269 (pttp) REVERT: C 582 LEU cc_start: 0.8902 (mt) cc_final: 0.8480 (mt) REVERT: C 584 HIS cc_start: 0.8484 (m90) cc_final: 0.8174 (m90) REVERT: C 603 MET cc_start: 0.7614 (mtt) cc_final: 0.7391 (mtt) REVERT: C 606 LEU cc_start: 0.8699 (mp) cc_final: 0.8422 (mp) REVERT: D 78 ASN cc_start: 0.8968 (t0) cc_final: 0.8207 (t0) REVERT: D 98 GLN cc_start: 0.6745 (pp30) cc_final: 0.5983 (tm-30) REVERT: D 103 HIS cc_start: 0.6708 (m-70) cc_final: 0.6401 (m-70) REVERT: D 140 LEU cc_start: 0.8996 (tt) cc_final: 0.8766 (tt) outliers start: 5 outliers final: 1 residues processed: 454 average time/residue: 0.2793 time to fit residues: 176.8579 Evaluate side-chains 409 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 407 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 95 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 98 optimal weight: 0.0070 chunk 150 optimal weight: 0.0870 chunk 84 optimal weight: 0.3980 chunk 8 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 459 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 357 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 594 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.157437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.122694 restraints weight = 29886.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.127144 restraints weight = 17314.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.130220 restraints weight = 11314.768| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14205 Z= 0.139 Angle : 0.672 11.194 19562 Z= 0.354 Chirality : 0.042 0.173 2195 Planarity : 0.004 0.056 2244 Dihedral : 21.064 169.156 2554 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.14 % Favored : 91.73 % Rotamer: Outliers : 0.07 % Allowed : 3.60 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1535 helix: 0.06 (0.21), residues: 590 sheet: -0.26 (0.36), residues: 224 loop : -1.68 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 259 HIS 0.012 0.001 HIS C 415 PHE 0.035 0.001 PHE A 192 TYR 0.028 0.002 TYR A 41 ARG 0.010 0.001 ARG A 355 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 580) hydrogen bonds : angle 5.06885 ( 1605) covalent geometry : bond 0.00297 (14204) covalent geometry : angle 0.67164 (19562) Misc. bond : bond 0.00106 ( 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 446 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 445 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9109 (mttt) cc_final: 0.8755 (mttp) REVERT: A 55 THR cc_start: 0.6979 (p) cc_final: 0.6698 (t) REVERT: A 65 ASP cc_start: 0.8585 (t70) cc_final: 0.8242 (t0) REVERT: A 66 PHE cc_start: 0.7332 (m-80) cc_final: 0.6970 (m-80) REVERT: A 119 ASP cc_start: 0.8679 (p0) cc_final: 0.8454 (p0) REVERT: A 164 MET cc_start: 0.9214 (ptp) cc_final: 0.8904 (ptp) REVERT: A 181 ARG cc_start: 0.8611 (ttp80) cc_final: 0.8248 (ttp80) REVERT: A 226 VAL cc_start: 0.8786 (p) cc_final: 0.8425 (p) REVERT: A 231 LYS cc_start: 0.8966 (mptt) cc_final: 0.8689 (mptt) REVERT: A 236 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8518 (tppt) REVERT: A 246 LYS cc_start: 0.7842 (pptt) cc_final: 0.7133 (tmtt) REVERT: A 255 LEU cc_start: 0.7748 (mt) cc_final: 0.7463 (mt) REVERT: A 290 ARG cc_start: 0.8368 (ppt170) cc_final: 0.8022 (pmt-80) REVERT: A 293 LYS cc_start: 0.7940 (pttm) cc_final: 0.7316 (pttm) REVERT: A 305 GLU cc_start: 0.8640 (tt0) cc_final: 0.7920 (tp30) REVERT: A 328 LEU cc_start: 0.8184 (mt) cc_final: 0.7941 (mt) REVERT: A 346 GLU cc_start: 0.7852 (mp0) cc_final: 0.7513 (mp0) REVERT: A 351 LYS cc_start: 0.8373 (tttp) cc_final: 0.7750 (tppt) REVERT: A 355 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7591 (ttm110) REVERT: A 368 LYS cc_start: 0.8849 (mtpt) cc_final: 0.8497 (mtpt) REVERT: A 369 ARG cc_start: 0.9090 (ptm-80) cc_final: 0.8670 (ptm-80) REVERT: A 370 LEU cc_start: 0.8922 (tt) cc_final: 0.8405 (tt) REVERT: A 380 LYS cc_start: 0.8326 (ttpt) cc_final: 0.8098 (ttmt) REVERT: A 406 TRP cc_start: 0.8785 (t60) cc_final: 0.8242 (t60) REVERT: A 409 TYR cc_start: 0.8670 (t80) cc_final: 0.8204 (t80) REVERT: A 426 TYR cc_start: 0.7009 (p90) cc_final: 0.6612 (p90) REVERT: A 489 ASN cc_start: 0.6953 (p0) cc_final: 0.6634 (p0) REVERT: A 498 GLU cc_start: 0.8189 (mp0) cc_final: 0.7948 (mp0) REVERT: A 502 LEU cc_start: 0.9123 (pp) cc_final: 0.8686 (pp) REVERT: A 516 VAL cc_start: 0.8811 (m) cc_final: 0.8222 (p) REVERT: A 518 ILE cc_start: 0.8963 (mp) cc_final: 0.8660 (tp) REVERT: A 520 ASN cc_start: 0.8777 (m-40) cc_final: 0.8410 (m-40) REVERT: A 525 ASN cc_start: 0.6704 (m-40) cc_final: 0.6156 (m110) REVERT: A 536 LYS cc_start: 0.8218 (tppt) cc_final: 0.8001 (tppt) REVERT: A 560 ILE cc_start: 0.8049 (mt) cc_final: 0.7735 (pt) REVERT: A 565 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 569 ASN cc_start: 0.6954 (m110) cc_final: 0.6680 (m110) REVERT: C 32 LEU cc_start: 0.7906 (mt) cc_final: 0.7694 (mt) REVERT: C 53 LYS cc_start: 0.7442 (mppt) cc_final: 0.6666 (tppt) REVERT: C 64 LEU cc_start: 0.7781 (tt) cc_final: 0.7292 (tt) REVERT: C 71 ASN cc_start: 0.7657 (m110) cc_final: 0.7404 (m110) REVERT: C 90 LYS cc_start: 0.8361 (ptmm) cc_final: 0.8104 (ptmm) REVERT: C 95 LYS cc_start: 0.9120 (mppt) cc_final: 0.8672 (mppt) REVERT: C 128 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7045 (mt-10) REVERT: C 139 LYS cc_start: 0.7536 (tmmt) cc_final: 0.7093 (ptmm) REVERT: C 144 GLU cc_start: 0.7116 (tp30) cc_final: 0.6726 (tp30) REVERT: C 164 MET cc_start: 0.8602 (ppp) cc_final: 0.8185 (ppp) REVERT: C 203 LYS cc_start: 0.7148 (ptpp) cc_final: 0.6929 (pttm) REVERT: C 204 TYR cc_start: 0.7642 (m-80) cc_final: 0.7338 (m-10) REVERT: C 236 LYS cc_start: 0.8677 (mppt) cc_final: 0.8108 (mppt) REVERT: C 244 GLN cc_start: 0.5926 (tp-100) cc_final: 0.5691 (tp40) REVERT: C 262 VAL cc_start: 0.8882 (m) cc_final: 0.8621 (p) REVERT: C 263 ARG cc_start: 0.8283 (ptt180) cc_final: 0.6873 (ptt180) REVERT: C 292 GLU cc_start: 0.8672 (pm20) cc_final: 0.8379 (pm20) REVERT: C 302 ASN cc_start: 0.8343 (t0) cc_final: 0.7930 (m110) REVERT: C 306 MET cc_start: 0.8027 (tmm) cc_final: 0.7590 (tmm) REVERT: C 308 ARG cc_start: 0.8671 (ttp-170) cc_final: 0.8143 (ttm-80) REVERT: C 316 MET cc_start: 0.7201 (mtt) cc_final: 0.6913 (mtt) REVERT: C 323 GLN cc_start: 0.8715 (mt0) cc_final: 0.8449 (mm-40) REVERT: C 351 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8772 (tttm) REVERT: C 365 ASP cc_start: 0.7939 (p0) cc_final: 0.7687 (p0) REVERT: C 382 HIS cc_start: 0.7989 (t70) cc_final: 0.7750 (t-90) REVERT: C 398 GLU cc_start: 0.8073 (tt0) cc_final: 0.7454 (tt0) REVERT: C 406 TRP cc_start: 0.8972 (t-100) cc_final: 0.8619 (t-100) REVERT: C 438 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7086 (tp30) REVERT: C 442 CYS cc_start: 0.6563 (p) cc_final: 0.6124 (m) REVERT: C 449 SER cc_start: 0.8670 (t) cc_final: 0.8466 (t) REVERT: C 464 GLU cc_start: 0.7096 (mp0) cc_final: 0.6718 (mp0) REVERT: C 476 PHE cc_start: 0.7940 (m-80) cc_final: 0.7657 (m-80) REVERT: C 494 LEU cc_start: 0.7949 (tp) cc_final: 0.7633 (tt) REVERT: C 504 GLU cc_start: 0.8485 (tp30) cc_final: 0.8020 (tp30) REVERT: C 536 LYS cc_start: 0.7847 (ttmt) cc_final: 0.7412 (ttmt) REVERT: C 550 LYS cc_start: 0.8353 (mttt) cc_final: 0.8110 (mttt) REVERT: C 557 LEU cc_start: 0.8849 (mm) cc_final: 0.8513 (mm) REVERT: C 566 LYS cc_start: 0.8655 (pttp) cc_final: 0.8246 (pttp) REVERT: C 582 LEU cc_start: 0.8893 (mt) cc_final: 0.8478 (mt) REVERT: C 584 HIS cc_start: 0.8474 (m90) cc_final: 0.8230 (m90) REVERT: C 603 MET cc_start: 0.7599 (mtt) cc_final: 0.7331 (mtt) REVERT: C 606 LEU cc_start: 0.8706 (mp) cc_final: 0.8431 (mp) REVERT: D 78 ASN cc_start: 0.8932 (t0) cc_final: 0.8448 (t0) REVERT: D 98 GLN cc_start: 0.6745 (pp30) cc_final: 0.6081 (tm-30) REVERT: D 103 HIS cc_start: 0.6759 (m-70) cc_final: 0.6432 (m-70) REVERT: D 140 LEU cc_start: 0.8961 (tt) cc_final: 0.8741 (tt) outliers start: 1 outliers final: 0 residues processed: 446 average time/residue: 0.2846 time to fit residues: 177.3068 Evaluate side-chains 402 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 129 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 143 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 415 HIS ** 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 = 0.4142 r_free = 0.4142 target = 0.156689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.121931 restraints weight = 30762.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.126318 restraints weight = 17783.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.129378 restraints weight = 11667.022| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14205 Z= 0.141 Angle : 0.682 11.795 19562 Z= 0.357 Chirality : 0.042 0.167 2195 Planarity : 0.005 0.071 2244 Dihedral : 21.054 169.680 2554 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.82 % Favored : 92.05 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1535 helix: 0.09 (0.21), residues: 589 sheet: -0.26 (0.36), residues: 219 loop : -1.64 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 241 HIS 0.010 0.001 HIS A 506 PHE 0.068 0.002 PHE A 589 TYR 0.033 0.002 TYR A 41 ARG 0.008 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 580) hydrogen bonds : angle 5.05366 ( 1605) covalent geometry : bond 0.00301 (14204) covalent geometry : angle 0.68213 (19562) Misc. bond : bond 0.00105 ( 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 440 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 1.414 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: 0.7693 (tpt) cc_final: 0.7339 (tpt) REVERT: A 2 LYS cc_start: 0.9121 (mttt) cc_final: 0.8458 (mttp) REVERT: A 51 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8235 (mtm-85) REVERT: A 65 ASP cc_start: 0.8584 (t70) cc_final: 0.8223 (t0) REVERT: A 66 PHE cc_start: 0.7222 (m-80) cc_final: 0.6891 (m-80) REVERT: A 119 ASP cc_start: 0.8689 (p0) cc_final: 0.8456 (p0) REVERT: A 181 ARG cc_start: 0.8562 (ttp80) cc_final: 0.8137 (ttp80) REVERT: A 226 VAL cc_start: 0.8811 (p) cc_final: 0.8456 (p) REVERT: A 231 LYS cc_start: 0.8995 (mptt) cc_final: 0.8694 (mptt) REVERT: A 246 LYS cc_start: 0.7860 (pptt) cc_final: 0.7088 (tmtt) REVERT: A 255 LEU cc_start: 0.7810 (mt) cc_final: 0.7502 (mt) REVERT: A 260 ASP cc_start: 0.7744 (p0) cc_final: 0.7500 (p0) REVERT: A 272 MET cc_start: 0.7942 (mtt) cc_final: 0.7597 (mtt) REVERT: A 290 ARG cc_start: 0.8431 (ppt170) cc_final: 0.8010 (pmt-80) REVERT: A 293 LYS cc_start: 0.7976 (pttm) cc_final: 0.7362 (pttm) REVERT: A 305 GLU cc_start: 0.8615 (tt0) cc_final: 0.7905 (tp30) REVERT: A 316 MET cc_start: 0.6810 (tmm) cc_final: 0.6257 (tmm) REVERT: A 320 HIS cc_start: 0.7231 (t-90) cc_final: 0.6580 (t-90) REVERT: A 323 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8324 (tm-30) REVERT: A 324 THR cc_start: 0.8161 (t) cc_final: 0.7873 (p) REVERT: A 328 LEU cc_start: 0.8172 (mt) cc_final: 0.7965 (mt) REVERT: A 330 THR cc_start: 0.8869 (m) cc_final: 0.8585 (p) REVERT: A 346 GLU cc_start: 0.7853 (mp0) cc_final: 0.7526 (mp0) REVERT: A 348 PHE cc_start: 0.8814 (t80) cc_final: 0.8489 (t80) REVERT: A 351 LYS cc_start: 0.8404 (tttp) cc_final: 0.7563 (ttmm) REVERT: A 355 ARG cc_start: 0.8386 (ttm110) cc_final: 0.7710 (ttm110) REVERT: A 368 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8500 (mtpt) REVERT: A 369 ARG cc_start: 0.9132 (ptm-80) cc_final: 0.8695 (ptm-80) REVERT: A 370 LEU cc_start: 0.8964 (tt) cc_final: 0.8551 (tt) REVERT: A 380 LYS cc_start: 0.8369 (ttpt) cc_final: 0.8099 (ttmt) REVERT: A 406 TRP cc_start: 0.8793 (t60) cc_final: 0.8228 (t60) REVERT: A 409 TYR cc_start: 0.8675 (t80) cc_final: 0.8206 (t80) REVERT: A 426 TYR cc_start: 0.7053 (p90) cc_final: 0.6653 (p90) REVERT: A 441 THR cc_start: 0.6858 (t) cc_final: 0.6457 (m) REVERT: A 489 ASN cc_start: 0.6981 (p0) cc_final: 0.6765 (p0) REVERT: A 498 GLU cc_start: 0.8211 (mp0) cc_final: 0.7939 (mp0) REVERT: A 502 LEU cc_start: 0.9093 (pp) cc_final: 0.8650 (pp) REVERT: A 516 VAL cc_start: 0.8806 (m) cc_final: 0.8311 (p) REVERT: A 520 ASN cc_start: 0.8808 (m-40) cc_final: 0.8534 (m-40) REVERT: A 525 ASN cc_start: 0.6798 (m-40) cc_final: 0.6198 (m-40) REVERT: A 560 ILE cc_start: 0.8076 (mt) cc_final: 0.7766 (pt) REVERT: A 565 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 569 ASN cc_start: 0.7029 (m110) cc_final: 0.6661 (m110) REVERT: B 136 LYS cc_start: 0.7937 (mptt) cc_final: 0.7226 (mptt) REVERT: B 143 ASN cc_start: 0.8248 (p0) cc_final: 0.7855 (p0) REVERT: C 30 LYS cc_start: 0.8106 (mttt) cc_final: 0.7858 (mttt) REVERT: C 53 LYS cc_start: 0.7401 (mppt) cc_final: 0.6660 (tppt) REVERT: C 71 ASN cc_start: 0.7677 (m110) cc_final: 0.7415 (m110) REVERT: C 95 LYS cc_start: 0.9125 (mppt) cc_final: 0.8688 (mppt) REVERT: C 128 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7019 (mt-10) REVERT: C 144 GLU cc_start: 0.7087 (tp30) cc_final: 0.6738 (tp30) REVERT: C 164 MET cc_start: 0.8600 (ppp) cc_final: 0.8327 (ppp) REVERT: C 199 TYR cc_start: 0.8051 (t80) cc_final: 0.7555 (t80) REVERT: C 203 LYS cc_start: 0.7278 (ptpp) cc_final: 0.6728 (ptpp) REVERT: C 204 TYR cc_start: 0.7719 (m-80) cc_final: 0.7443 (m-10) REVERT: C 225 CYS cc_start: 0.8538 (m) cc_final: 0.8322 (m) REVERT: C 232 ILE cc_start: 0.7921 (mp) cc_final: 0.7719 (mp) REVERT: C 236 LYS cc_start: 0.8719 (mppt) cc_final: 0.8147 (mppt) REVERT: C 244 GLN cc_start: 0.5999 (tp-100) cc_final: 0.5720 (tp40) REVERT: C 262 VAL cc_start: 0.8886 (m) cc_final: 0.8623 (p) REVERT: C 263 ARG cc_start: 0.8280 (ptt180) cc_final: 0.6922 (ptt180) REVERT: C 292 GLU cc_start: 0.8671 (pm20) cc_final: 0.8392 (pm20) REVERT: C 302 ASN cc_start: 0.8289 (t0) cc_final: 0.7953 (m110) REVERT: C 306 MET cc_start: 0.8076 (tmm) cc_final: 0.7533 (tmm) REVERT: C 316 MET cc_start: 0.7261 (mtt) cc_final: 0.6979 (mtt) REVERT: C 323 GLN cc_start: 0.8742 (mt0) cc_final: 0.8484 (mm-40) REVERT: C 344 TYR cc_start: 0.8917 (m-10) cc_final: 0.8676 (m-10) REVERT: C 351 LYS cc_start: 0.9045 (ttmm) cc_final: 0.8651 (mtpp) REVERT: C 357 GLN cc_start: 0.8000 (tt0) cc_final: 0.7331 (tt0) REVERT: C 362 TYR cc_start: 0.8053 (m-10) cc_final: 0.7830 (m-10) REVERT: C 365 ASP cc_start: 0.7961 (p0) cc_final: 0.7726 (p0) REVERT: C 406 TRP cc_start: 0.8864 (t-100) cc_final: 0.8592 (t-100) REVERT: C 438 GLU cc_start: 0.7772 (mm-30) cc_final: 0.7154 (tp30) REVERT: C 442 CYS cc_start: 0.6550 (p) cc_final: 0.6125 (m) REVERT: C 476 PHE cc_start: 0.8004 (m-80) cc_final: 0.7713 (m-80) REVERT: C 504 GLU cc_start: 0.8455 (tp30) cc_final: 0.8005 (tp30) REVERT: C 536 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7433 (ttmt) REVERT: C 550 LYS cc_start: 0.8356 (mttt) cc_final: 0.8117 (mttt) REVERT: C 557 LEU cc_start: 0.8876 (mm) cc_final: 0.8529 (mm) REVERT: C 566 LYS cc_start: 0.8690 (pttp) cc_final: 0.8281 (pttp) REVERT: C 582 LEU cc_start: 0.8905 (mt) cc_final: 0.8525 (mt) REVERT: C 584 HIS cc_start: 0.8497 (m90) cc_final: 0.8234 (m90) REVERT: C 603 MET cc_start: 0.7718 (mtt) cc_final: 0.7417 (mtt) REVERT: C 606 LEU cc_start: 0.8709 (mp) cc_final: 0.8450 (mp) REVERT: D 14 TRP cc_start: 0.6246 (m-10) cc_final: 0.6005 (m-10) REVERT: D 78 ASN cc_start: 0.8954 (t0) cc_final: 0.8276 (t0) REVERT: D 98 GLN cc_start: 0.6702 (pp30) cc_final: 0.6171 (tm-30) REVERT: D 103 HIS cc_start: 0.6889 (m-70) cc_final: 0.6552 (m-70) REVERT: D 157 LEU cc_start: 0.8535 (mm) cc_final: 0.8257 (mm) REVERT: D 159 GLU cc_start: 0.8267 (mp0) cc_final: 0.8038 (mp0) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.3169 time to fit residues: 197.8946 Evaluate side-chains 411 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 34 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.155539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.120543 restraints weight = 30744.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.124936 restraints weight = 17821.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.127972 restraints weight = 11692.647| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.3448 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= 0.155 Angle : 0.700 12.357 19562 Z= 0.368 Chirality : 0.042 0.166 2195 Planarity : 0.005 0.060 2244 Dihedral : 21.069 170.071 2554 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.21 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1535 helix: 0.07 (0.21), residues: 590 sheet: -0.41 (0.35), residues: 242 loop : -1.63 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 363 HIS 0.008 0.001 HIS A 506 PHE 0.024 0.001 PHE A 192 TYR 0.020 0.002 TYR A 595 ARG 0.010 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04279 ( 580) hydrogen bonds : angle 5.09644 ( 1605) covalent geometry : bond 0.00326 (14204) covalent geometry : angle 0.69989 (19562) Misc. bond : bond 0.00114 ( 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 443 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 1.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 LYS cc_start: 0.9118 (mttt) cc_final: 0.8842 (mttp) REVERT: A 65 ASP cc_start: 0.8598 (t70) cc_final: 0.8206 (t0) REVERT: A 66 PHE cc_start: 0.7250 (m-80) cc_final: 0.6849 (m-80) REVERT: A 119 ASP cc_start: 0.8782 (p0) cc_final: 0.8575 (p0) REVERT: A 181 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8212 (ttp80) REVERT: A 222 LEU cc_start: 0.8897 (tp) cc_final: 0.8686 (tp) REVERT: A 226 VAL cc_start: 0.8873 (p) cc_final: 0.8526 (p) REVERT: A 231 LYS cc_start: 0.9003 (mptt) cc_final: 0.8695 (mptt) REVERT: A 246 LYS cc_start: 0.7931 (pptt) cc_final: 0.7162 (tmtt) REVERT: A 255 LEU cc_start: 0.7883 (mt) cc_final: 0.7538 (mt) REVERT: A 260 ASP cc_start: 0.7777 (p0) cc_final: 0.7531 (p0) REVERT: A 272 MET cc_start: 0.8036 (mtt) cc_final: 0.7688 (mtt) REVERT: A 290 ARG cc_start: 0.8433 (ppt170) cc_final: 0.8038 (pmt-80) REVERT: A 293 LYS cc_start: 0.7986 (pttm) cc_final: 0.7355 (pttm) REVERT: A 305 GLU cc_start: 0.8636 (tt0) cc_final: 0.7899 (tp30) REVERT: A 316 MET cc_start: 0.6789 (tmm) cc_final: 0.6390 (tmm) REVERT: A 320 HIS cc_start: 0.7372 (t-90) cc_final: 0.6886 (t-170) REVERT: A 324 THR cc_start: 0.8158 (t) cc_final: 0.7746 (t) REVERT: A 346 GLU cc_start: 0.7834 (mp0) cc_final: 0.7518 (mp0) REVERT: A 348 PHE cc_start: 0.8862 (t80) cc_final: 0.8498 (t80) REVERT: A 351 LYS cc_start: 0.8465 (tttp) cc_final: 0.8181 (ttmm) REVERT: A 368 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8476 (mtpt) REVERT: A 369 ARG cc_start: 0.9142 (ptm-80) cc_final: 0.8706 (ptm-80) REVERT: A 370 LEU cc_start: 0.8989 (tt) cc_final: 0.8550 (tt) REVERT: A 379 ARG cc_start: 0.7850 (mtp85) cc_final: 0.7565 (mtp85) REVERT: A 382 HIS cc_start: 0.7399 (t-90) cc_final: 0.7140 (t-90) REVERT: A 406 TRP cc_start: 0.8810 (t60) cc_final: 0.8269 (t60) REVERT: A 409 TYR cc_start: 0.8685 (t80) cc_final: 0.8213 (t80) REVERT: A 426 TYR cc_start: 0.7051 (p90) cc_final: 0.6692 (p90) REVERT: A 482 LYS cc_start: 0.7772 (mmmm) cc_final: 0.7101 (mmmm) REVERT: A 489 ASN cc_start: 0.6987 (p0) cc_final: 0.6740 (p0) REVERT: A 502 LEU cc_start: 0.9093 (pp) cc_final: 0.8640 (pp) REVERT: A 516 VAL cc_start: 0.8804 (m) cc_final: 0.8269 (p) REVERT: A 520 ASN cc_start: 0.8783 (m-40) cc_final: 0.8417 (m-40) REVERT: A 525 ASN cc_start: 0.6774 (m-40) cc_final: 0.6197 (m-40) REVERT: A 560 ILE cc_start: 0.8151 (mt) cc_final: 0.7806 (pt) REVERT: A 565 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7665 (mt-10) REVERT: A 569 ASN cc_start: 0.7143 (m110) cc_final: 0.6778 (m110) REVERT: A 585 THR cc_start: 0.8028 (p) cc_final: 0.7754 (t) REVERT: B 128 LYS cc_start: 0.8415 (tttm) cc_final: 0.7964 (tttm) REVERT: B 136 LYS cc_start: 0.7845 (mptt) cc_final: 0.7233 (mptt) REVERT: B 143 ASN cc_start: 0.8290 (p0) cc_final: 0.7812 (p0) REVERT: C 15 GLN cc_start: 0.8362 (pp30) cc_final: 0.8146 (pp30) REVERT: C 30 LYS cc_start: 0.8120 (mttt) cc_final: 0.7842 (mttt) REVERT: C 32 LEU cc_start: 0.7923 (mt) cc_final: 0.7577 (mt) REVERT: C 53 LYS cc_start: 0.7082 (mppt) cc_final: 0.6501 (mppt) REVERT: C 71 ASN cc_start: 0.7710 (m110) cc_final: 0.7425 (m110) REVERT: C 95 LYS cc_start: 0.9130 (mppt) cc_final: 0.8724 (mppt) REVERT: C 159 ASP cc_start: 0.7551 (t0) cc_final: 0.7097 (t0) REVERT: C 164 MET cc_start: 0.8568 (ppp) cc_final: 0.8289 (ppp) REVERT: C 199 TYR cc_start: 0.8030 (t80) cc_final: 0.7637 (t80) REVERT: C 204 TYR cc_start: 0.7764 (m-80) cc_final: 0.7426 (m-10) REVERT: C 236 LYS cc_start: 0.8745 (mppt) cc_final: 0.8161 (mppt) REVERT: C 244 GLN cc_start: 0.6005 (tp-100) cc_final: 0.5743 (tp-100) REVERT: C 262 VAL cc_start: 0.8889 (m) cc_final: 0.8649 (p) REVERT: C 263 ARG cc_start: 0.8290 (ptt180) cc_final: 0.6988 (ptt180) REVERT: C 299 LEU cc_start: 0.8310 (mt) cc_final: 0.8093 (mt) REVERT: C 302 ASN cc_start: 0.8313 (t0) cc_final: 0.7914 (m110) REVERT: C 306 MET cc_start: 0.8092 (tmm) cc_final: 0.7632 (tmm) REVERT: C 316 MET cc_start: 0.7281 (mtt) cc_final: 0.7041 (mtt) REVERT: C 351 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8760 (tttm) REVERT: C 365 ASP cc_start: 0.7978 (p0) cc_final: 0.7752 (p0) REVERT: C 406 TRP cc_start: 0.8802 (t-100) cc_final: 0.8572 (t-100) REVERT: C 438 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7427 (tp30) REVERT: C 442 CYS cc_start: 0.6524 (p) cc_final: 0.6155 (m) REVERT: C 465 GLU cc_start: 0.7074 (tp30) cc_final: 0.6815 (tp30) REVERT: C 476 PHE cc_start: 0.8026 (m-80) cc_final: 0.7726 (m-80) REVERT: C 504 GLU cc_start: 0.8428 (tp30) cc_final: 0.8072 (tp30) REVERT: C 536 LYS cc_start: 0.7870 (ttmt) cc_final: 0.7458 (ttmt) REVERT: C 549 TYR cc_start: 0.7631 (m-80) cc_final: 0.7427 (m-80) REVERT: C 550 LYS cc_start: 0.8368 (mttt) cc_final: 0.8127 (mttt) REVERT: C 557 LEU cc_start: 0.8897 (mm) cc_final: 0.8542 (mm) REVERT: C 566 LYS cc_start: 0.8735 (pttp) cc_final: 0.8313 (pttp) REVERT: C 582 LEU cc_start: 0.8916 (mt) cc_final: 0.8541 (mt) REVERT: C 584 HIS cc_start: 0.8561 (m90) cc_final: 0.8289 (m90) REVERT: C 603 MET cc_start: 0.7782 (mtt) cc_final: 0.7478 (mtt) REVERT: C 606 LEU cc_start: 0.8728 (mp) cc_final: 0.8472 (mp) REVERT: D 18 ASP cc_start: 0.6362 (m-30) cc_final: 0.6127 (m-30) REVERT: D 32 ASN cc_start: 0.9117 (t0) cc_final: 0.8892 (t0) REVERT: D 78 ASN cc_start: 0.8979 (t0) cc_final: 0.8620 (t0) REVERT: D 103 HIS cc_start: 0.6929 (m-70) cc_final: 0.6610 (m-70) REVERT: D 157 LEU cc_start: 0.8526 (mm) cc_final: 0.8181 (mm) REVERT: D 159 GLU cc_start: 0.8279 (mp0) cc_final: 0.8074 (mp0) outliers start: 0 outliers final: 0 residues processed: 443 average time/residue: 0.2884 time to fit residues: 177.9163 Evaluate side-chains 410 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 96 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 139 optimal weight: 0.4980 chunk 136 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 55 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 GLN ** C 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** C 428 GLN ** 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 = 0.4132 r_free = 0.4132 target = 0.155895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.121114 restraints weight = 30263.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.125573 restraints weight = 17537.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.128636 restraints weight = 11440.084| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14205 Z= 0.145 Angle : 0.702 12.974 19562 Z= 0.368 Chirality : 0.042 0.162 2195 Planarity : 0.004 0.055 2244 Dihedral : 21.071 169.707 2554 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.08 % Favored : 91.86 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.21), residues: 1535 helix: 0.11 (0.21), residues: 589 sheet: -0.36 (0.35), residues: 237 loop : -1.66 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 14 HIS 0.009 0.001 HIS A 506 PHE 0.075 0.002 PHE A 589 TYR 0.028 0.002 TYR A 41 ARG 0.010 0.001 ARG A 472 Details of bonding type rmsd hydrogen bonds : bond 0.04235 ( 580) hydrogen bonds : angle 5.05715 ( 1605) covalent geometry : bond 0.00312 (14204) covalent geometry : angle 0.70162 (19562) Misc. bond : bond 0.00106 ( 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 440 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 440 time to evaluate : 1.287 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: A 2 LYS cc_start: 0.9118 (mttt) cc_final: 0.8862 (mttp) REVERT: A 65 ASP cc_start: 0.8591 (t70) cc_final: 0.8200 (t0) REVERT: A 66 PHE cc_start: 0.7228 (m-80) cc_final: 0.6838 (m-80) REVERT: A 119 ASP cc_start: 0.8804 (p0) cc_final: 0.8584 (p0) REVERT: A 181 ARG cc_start: 0.8617 (ttp80) cc_final: 0.8177 (ttp80) REVERT: A 222 LEU cc_start: 0.8886 (tp) cc_final: 0.8676 (tp) REVERT: A 226 VAL cc_start: 0.8867 (p) cc_final: 0.8498 (p) REVERT: A 231 LYS cc_start: 0.9004 (mptt) cc_final: 0.8686 (mptt) REVERT: A 255 LEU cc_start: 0.7879 (mt) cc_final: 0.7553 (mt) REVERT: A 260 ASP cc_start: 0.7762 (p0) cc_final: 0.7530 (p0) REVERT: A 272 MET cc_start: 0.8033 (mtt) cc_final: 0.7377 (mtt) REVERT: A 275 ASN cc_start: 0.8709 (m110) cc_final: 0.8338 (m110) REVERT: A 290 ARG cc_start: 0.8435 (ppt170) cc_final: 0.8025 (pmt-80) REVERT: A 293 LYS cc_start: 0.7988 (pttm) cc_final: 0.7341 (pttm) REVERT: A 305 GLU cc_start: 0.8651 (tt0) cc_final: 0.7884 (tp30) REVERT: A 316 MET cc_start: 0.6778 (tmm) cc_final: 0.6346 (tmm) REVERT: A 320 HIS cc_start: 0.7405 (t-90) cc_final: 0.6788 (t-170) REVERT: A 324 THR cc_start: 0.8119 (t) cc_final: 0.7794 (p) REVERT: A 330 THR cc_start: 0.8926 (m) cc_final: 0.8608 (p) REVERT: A 346 GLU cc_start: 0.7824 (mp0) cc_final: 0.7519 (mp0) REVERT: A 348 PHE cc_start: 0.8873 (t80) cc_final: 0.8470 (t80) REVERT: A 351 LYS cc_start: 0.8553 (tttp) cc_final: 0.7639 (ttmm) REVERT: A 355 ARG cc_start: 0.8449 (ttm110) cc_final: 0.7757 (ttm110) REVERT: A 368 LYS cc_start: 0.8821 (mtpt) cc_final: 0.8481 (mtpt) REVERT: A 369 ARG cc_start: 0.9126 (ptm-80) cc_final: 0.8701 (ptm-80) REVERT: A 370 LEU cc_start: 0.8993 (tt) cc_final: 0.8536 (tt) REVERT: A 382 HIS cc_start: 0.7414 (t-90) cc_final: 0.7111 (t-90) REVERT: A 406 TRP cc_start: 0.8786 (t60) cc_final: 0.8255 (t60) REVERT: A 409 TYR cc_start: 0.8679 (t80) cc_final: 0.8177 (t80) REVERT: A 426 TYR cc_start: 0.7042 (p90) cc_final: 0.6720 (p90) REVERT: A 441 THR cc_start: 0.6880 (t) cc_final: 0.6472 (m) REVERT: A 482 LYS cc_start: 0.7762 (mmmm) cc_final: 0.7150 (mmmm) REVERT: A 489 ASN cc_start: 0.6968 (p0) cc_final: 0.6744 (p0) REVERT: A 498 GLU cc_start: 0.8229 (mp0) cc_final: 0.7998 (mp0) REVERT: A 502 LEU cc_start: 0.9089 (pp) cc_final: 0.8638 (pp) REVERT: A 516 VAL cc_start: 0.8814 (m) cc_final: 0.8318 (p) REVERT: A 520 ASN cc_start: 0.8810 (m-40) cc_final: 0.8430 (m-40) REVERT: A 525 ASN cc_start: 0.6784 (m-40) cc_final: 0.6209 (m-40) REVERT: A 560 ILE cc_start: 0.8116 (mt) cc_final: 0.7785 (pt) REVERT: A 565 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7644 (mt-10) REVERT: A 569 ASN cc_start: 0.7174 (m110) cc_final: 0.6845 (m110) REVERT: B 106 CYS cc_start: 0.7457 (t) cc_final: 0.6708 (m) REVERT: B 128 LYS cc_start: 0.8424 (tttm) cc_final: 0.7981 (tttm) REVERT: B 136 LYS cc_start: 0.7918 (mptt) cc_final: 0.7198 (mptt) REVERT: B 143 ASN cc_start: 0.8254 (p0) cc_final: 0.7773 (p0) REVERT: C 30 LYS cc_start: 0.8095 (mttt) cc_final: 0.7854 (mttt) REVERT: C 32 LEU cc_start: 0.7948 (mt) cc_final: 0.7641 (mt) REVERT: C 41 TYR cc_start: 0.7162 (p90) cc_final: 0.6828 (p90) REVERT: C 53 LYS cc_start: 0.7025 (mppt) cc_final: 0.6412 (mppt) REVERT: C 62 MET cc_start: 0.6251 (tpt) cc_final: 0.5937 (tpt) REVERT: C 71 ASN cc_start: 0.7717 (m110) cc_final: 0.7431 (m110) REVERT: C 95 LYS cc_start: 0.9116 (mppt) cc_final: 0.8703 (mppt) REVERT: C 98 MET cc_start: 0.7407 (ttm) cc_final: 0.7010 (ttm) REVERT: C 144 GLU cc_start: 0.7112 (tp30) cc_final: 0.6779 (tp30) REVERT: C 159 ASP cc_start: 0.7501 (t0) cc_final: 0.7028 (t0) REVERT: C 164 MET cc_start: 0.8543 (ppp) cc_final: 0.8259 (ppp) REVERT: C 199 TYR cc_start: 0.7980 (t80) cc_final: 0.7636 (t80) REVERT: C 204 TYR cc_start: 0.7768 (m-80) cc_final: 0.7415 (m-10) REVERT: C 218 GLN cc_start: 0.7537 (mt0) cc_final: 0.7095 (mt0) REVERT: C 225 CYS cc_start: 0.8568 (m) cc_final: 0.8366 (m) REVERT: C 236 LYS cc_start: 0.8739 (mppt) cc_final: 0.8175 (mppt) REVERT: C 244 GLN cc_start: 0.6007 (tp-100) cc_final: 0.5731 (tp-100) REVERT: C 262 VAL cc_start: 0.8892 (m) cc_final: 0.8658 (p) REVERT: C 263 ARG cc_start: 0.8295 (ptt180) cc_final: 0.7004 (ptt180) REVERT: C 305 GLU cc_start: 0.8052 (tp30) cc_final: 0.7751 (tp30) REVERT: C 306 MET cc_start: 0.8070 (tmm) cc_final: 0.7651 (tmm) REVERT: C 316 MET cc_start: 0.7335 (mtt) cc_final: 0.7099 (mtt) REVERT: C 351 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8771 (tttm) REVERT: C 365 ASP cc_start: 0.7982 (p0) cc_final: 0.7749 (p0) REVERT: C 406 TRP cc_start: 0.8717 (t-100) cc_final: 0.8447 (t-100) REVERT: C 410 GLU cc_start: 0.8339 (tt0) cc_final: 0.7960 (tt0) REVERT: C 438 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7426 (tp30) REVERT: C 442 CYS cc_start: 0.6524 (p) cc_final: 0.6146 (m) REVERT: C 449 SER cc_start: 0.8645 (t) cc_final: 0.8443 (t) REVERT: C 464 GLU cc_start: 0.6869 (mp0) cc_final: 0.6620 (mp0) REVERT: C 465 GLU cc_start: 0.7117 (tp30) cc_final: 0.6826 (tp30) REVERT: C 476 PHE cc_start: 0.7970 (m-80) cc_final: 0.7674 (m-80) REVERT: C 504 GLU cc_start: 0.8394 (tp30) cc_final: 0.7970 (tp30) REVERT: C 536 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7469 (ttmt) REVERT: C 550 LYS cc_start: 0.8358 (mttt) cc_final: 0.8135 (mttt) REVERT: C 557 LEU cc_start: 0.8965 (mm) cc_final: 0.8725 (mm) REVERT: C 566 LYS cc_start: 0.8719 (pttp) cc_final: 0.8296 (pttp) REVERT: C 582 LEU cc_start: 0.8883 (mt) cc_final: 0.8498 (mt) REVERT: C 584 HIS cc_start: 0.8560 (m90) cc_final: 0.8284 (m90) REVERT: C 603 MET cc_start: 0.7708 (mtt) cc_final: 0.7422 (mtt) REVERT: C 606 LEU cc_start: 0.8725 (mp) cc_final: 0.8470 (mp) REVERT: D 18 ASP cc_start: 0.6256 (m-30) cc_final: 0.6055 (m-30) REVERT: D 78 ASN cc_start: 0.8939 (t0) cc_final: 0.8308 (t0) REVERT: D 103 HIS cc_start: 0.6860 (m-70) cc_final: 0.6570 (m-70) REVERT: D 157 LEU cc_start: 0.8516 (mm) cc_final: 0.8156 (mm) REVERT: D 158 ILE cc_start: 0.8871 (tt) cc_final: 0.8607 (tt) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.2745 time to fit residues: 168.9859 Evaluate side-chains 401 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 149 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 143 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 ASN A 196 GLN ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS C 428 GLN ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.155498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.120663 restraints weight = 30219.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.125119 restraints weight = 17577.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.128155 restraints weight = 11513.403| |-----------------------------------------------------------------------------| r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3835 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 : 0.700 12.841 19562 Z= 0.366 Chirality : 0.043 0.176 2195 Planarity : 0.005 0.055 2244 Dihedral : 21.053 170.180 2554 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1535 helix: 0.13 (0.21), residues: 590 sheet: -0.51 (0.35), residues: 236 loop : -1.61 (0.24), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 363 HIS 0.010 0.001 HIS A 506 PHE 0.026 0.001 PHE A 589 TYR 0.024 0.002 TYR C 578 ARG 0.012 0.001 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 580) hydrogen bonds : angle 5.02705 ( 1605) covalent geometry : bond 0.00320 (14204) covalent geometry : angle 0.70047 (19562) Misc. bond : bond 0.00107 ( 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 444 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7755 (tpt) cc_final: 0.7550 (tpt) REVERT: A 2 LYS cc_start: 0.9111 (mttt) cc_final: 0.8867 (mttp) REVERT: A 65 ASP cc_start: 0.8595 (t70) cc_final: 0.8205 (t0) REVERT: A 66 PHE cc_start: 0.7254 (m-80) cc_final: 0.6863 (m-80) REVERT: A 90 LYS cc_start: 0.7869 (pptt) cc_final: 0.7441 (ptmm) REVERT: A 226 VAL cc_start: 0.8874 (p) cc_final: 0.8499 (p) REVERT: A 231 LYS cc_start: 0.9013 (mptt) cc_final: 0.8718 (mptt) REVERT: A 255 LEU cc_start: 0.7909 (mt) cc_final: 0.7592 (mt) REVERT: A 260 ASP cc_start: 0.7785 (p0) cc_final: 0.7556 (p0) REVERT: A 272 MET cc_start: 0.8041 (mtt) cc_final: 0.7379 (mtt) REVERT: A 275 ASN cc_start: 0.8740 (m110) cc_final: 0.8399 (m110) REVERT: A 293 LYS cc_start: 0.8030 (pttm) cc_final: 0.7375 (pttm) REVERT: A 305 GLU cc_start: 0.8669 (tt0) cc_final: 0.7930 (tp30) REVERT: A 316 MET cc_start: 0.6730 (tmm) cc_final: 0.6059 (tmm) REVERT: A 320 HIS cc_start: 0.7477 (t-90) cc_final: 0.6768 (t-90) REVERT: A 324 THR cc_start: 0.8184 (t) cc_final: 0.7884 (p) REVERT: A 328 LEU cc_start: 0.8194 (mt) cc_final: 0.7961 (mt) REVERT: A 330 THR cc_start: 0.8950 (m) cc_final: 0.8624 (p) REVERT: A 346 GLU cc_start: 0.7844 (mp0) cc_final: 0.7528 (mp0) REVERT: A 351 LYS cc_start: 0.8588 (tttp) cc_final: 0.7750 (mmtm) REVERT: A 355 ARG cc_start: 0.8487 (ttm110) cc_final: 0.7802 (ttm110) REVERT: A 368 LYS cc_start: 0.8820 (mtpt) cc_final: 0.8475 (mtpt) REVERT: A 369 ARG cc_start: 0.9148 (ptm-80) cc_final: 0.8736 (ptm-80) REVERT: A 370 LEU cc_start: 0.8989 (tt) cc_final: 0.8506 (tt) REVERT: A 382 HIS cc_start: 0.7539 (t-90) cc_final: 0.7200 (t-90) REVERT: A 406 TRP cc_start: 0.8777 (t60) cc_final: 0.7332 (t60) REVERT: A 409 TYR cc_start: 0.8678 (t80) cc_final: 0.8204 (t80) REVERT: A 426 TYR cc_start: 0.7025 (p90) cc_final: 0.6709 (p90) REVERT: A 441 THR cc_start: 0.6930 (t) cc_final: 0.6545 (m) REVERT: A 482 LYS cc_start: 0.7809 (mmmm) cc_final: 0.7174 (mmmm) REVERT: A 489 ASN cc_start: 0.6975 (p0) cc_final: 0.6714 (p0) REVERT: A 498 GLU cc_start: 0.8236 (mp0) cc_final: 0.8015 (mp0) REVERT: A 502 LEU cc_start: 0.9074 (pp) cc_final: 0.8628 (pp) REVERT: A 516 VAL cc_start: 0.8815 (m) cc_final: 0.8354 (p) REVERT: A 520 ASN cc_start: 0.8807 (m-40) cc_final: 0.8473 (m-40) REVERT: A 525 ASN cc_start: 0.6808 (m-40) cc_final: 0.6207 (m-40) REVERT: A 560 ILE cc_start: 0.8161 (mt) cc_final: 0.7930 (pt) REVERT: A 565 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7648 (mt-10) REVERT: A 569 ASN cc_start: 0.7220 (m110) cc_final: 0.6848 (m110) REVERT: B 106 CYS cc_start: 0.7520 (t) cc_final: 0.6726 (m) REVERT: B 128 LYS cc_start: 0.8421 (tttm) cc_final: 0.7986 (tttm) REVERT: B 136 LYS cc_start: 0.7865 (mptt) cc_final: 0.7158 (mptt) REVERT: B 143 ASN cc_start: 0.8226 (p0) cc_final: 0.7885 (p0) REVERT: C 30 LYS cc_start: 0.8126 (mttt) cc_final: 0.7926 (mttt) REVERT: C 32 LEU cc_start: 0.7912 (mt) cc_final: 0.7578 (mt) REVERT: C 41 TYR cc_start: 0.7191 (p90) cc_final: 0.6853 (p90) REVERT: C 53 LYS cc_start: 0.7005 (mppt) cc_final: 0.6390 (mppt) REVERT: C 62 MET cc_start: 0.6415 (tpt) cc_final: 0.6087 (tpt) REVERT: C 71 ASN cc_start: 0.7704 (m110) cc_final: 0.7415 (m110) REVERT: C 84 GLN cc_start: 0.7899 (mp10) cc_final: 0.6978 (mp10) REVERT: C 95 LYS cc_start: 0.9115 (mppt) cc_final: 0.8701 (mppt) REVERT: C 98 MET cc_start: 0.7486 (ttm) cc_final: 0.7128 (ttm) REVERT: C 144 GLU cc_start: 0.7126 (tp30) cc_final: 0.6819 (tp30) REVERT: C 159 ASP cc_start: 0.7557 (t0) cc_final: 0.7057 (t0) REVERT: C 164 MET cc_start: 0.8554 (ppp) cc_final: 0.8273 (ppp) REVERT: C 199 TYR cc_start: 0.7962 (t80) cc_final: 0.7614 (t80) REVERT: C 204 TYR cc_start: 0.7817 (m-80) cc_final: 0.7436 (m-10) REVERT: C 218 GLN cc_start: 0.7532 (mt0) cc_final: 0.7010 (mt0) REVERT: C 225 CYS cc_start: 0.8630 (m) cc_final: 0.8389 (m) REVERT: C 236 LYS cc_start: 0.8749 (mppt) cc_final: 0.8216 (mppt) REVERT: C 244 GLN cc_start: 0.6058 (tp-100) cc_final: 0.5772 (tp-100) REVERT: C 292 GLU cc_start: 0.8699 (pm20) cc_final: 0.8388 (pm20) REVERT: C 305 GLU cc_start: 0.8036 (tp30) cc_final: 0.7735 (tp30) REVERT: C 306 MET cc_start: 0.8103 (tmm) cc_final: 0.7700 (tmm) REVERT: C 316 MET cc_start: 0.7395 (mtt) cc_final: 0.7178 (mtt) REVERT: C 351 LYS cc_start: 0.9043 (ttmm) cc_final: 0.8746 (tttm) REVERT: C 365 ASP cc_start: 0.7943 (p0) cc_final: 0.7687 (p0) REVERT: C 369 ARG cc_start: 0.8471 (mmp-170) cc_final: 0.8239 (mmp-170) REVERT: C 410 GLU cc_start: 0.8310 (tt0) cc_final: 0.7919 (tt0) REVERT: C 438 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7528 (tp30) REVERT: C 442 CYS cc_start: 0.6506 (p) cc_final: 0.6207 (m) REVERT: C 464 GLU cc_start: 0.6889 (mp0) cc_final: 0.6575 (mp0) REVERT: C 465 GLU cc_start: 0.7083 (tp30) cc_final: 0.6778 (tp30) REVERT: C 476 PHE cc_start: 0.8017 (m-80) cc_final: 0.7727 (m-80) REVERT: C 504 GLU cc_start: 0.8358 (tp30) cc_final: 0.7986 (tp30) REVERT: C 536 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7497 (ttmt) REVERT: C 550 LYS cc_start: 0.8379 (mttt) cc_final: 0.8163 (mttt) REVERT: C 555 LEU cc_start: 0.8273 (mm) cc_final: 0.7997 (mm) REVERT: C 557 LEU cc_start: 0.8989 (mm) cc_final: 0.8727 (mm) REVERT: C 566 LYS cc_start: 0.8728 (pttp) cc_final: 0.8355 (pttp) REVERT: C 579 ARG cc_start: 0.8128 (mmm160) cc_final: 0.7902 (mmp80) REVERT: C 584 HIS cc_start: 0.8516 (m90) cc_final: 0.8242 (m90) REVERT: C 603 MET cc_start: 0.7681 (mtt) cc_final: 0.7388 (mtt) REVERT: C 606 LEU cc_start: 0.8729 (mp) cc_final: 0.8479 (mp) REVERT: D 32 ASN cc_start: 0.9056 (t0) cc_final: 0.8799 (t0) REVERT: D 78 ASN cc_start: 0.8966 (t0) cc_final: 0.8575 (t0) REVERT: D 89 GLN cc_start: 0.8870 (mm110) cc_final: 0.8667 (mm110) REVERT: D 103 HIS cc_start: 0.6824 (m-70) cc_final: 0.6511 (m-70) REVERT: D 126 LYS cc_start: 0.8186 (tptp) cc_final: 0.7694 (tptp) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2796 time to fit residues: 174.9015 Evaluate side-chains 410 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 91 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 131 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** 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 = 0.4129 r_free = 0.4129 target = 0.155370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.120707 restraints weight = 30203.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125071 restraints weight = 17571.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.128081 restraints weight = 11650.801| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14205 Z= 0.150 Angle : 0.732 12.731 19562 Z= 0.381 Chirality : 0.043 0.176 2195 Planarity : 0.005 0.055 2244 Dihedral : 21.068 170.018 2554 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.27 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.21), residues: 1535 helix: 0.10 (0.21), residues: 591 sheet: -0.50 (0.35), residues: 231 loop : -1.64 (0.23), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP C 259 HIS 0.013 0.001 HIS C 506 PHE 0.035 0.002 PHE A 589 TYR 0.028 0.002 TYR A 41 ARG 0.012 0.001 ARG D 46 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 580) hydrogen bonds : angle 5.06103 ( 1605) covalent geometry : bond 0.00325 (14204) covalent geometry : angle 0.73151 (19562) Misc. bond : bond 0.00100 ( 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 442 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 1.383 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 1 MET cc_start: 0.7775 (tpt) cc_final: 0.7288 (tpt) REVERT: A 2 LYS cc_start: 0.9107 (mttt) cc_final: 0.8489 (mttp) REVERT: A 51 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8247 (mtm-85) REVERT: A 62 MET cc_start: 0.6131 (tmm) cc_final: 0.5923 (tmm) REVERT: A 65 ASP cc_start: 0.8592 (t70) cc_final: 0.8193 (t0) REVERT: A 66 PHE cc_start: 0.7211 (m-80) cc_final: 0.6857 (m-80) REVERT: A 90 LYS cc_start: 0.7854 (pptt) cc_final: 0.7421 (ptmm) REVERT: A 181 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8183 (ttp80) REVERT: A 196 GLN cc_start: 0.8005 (tm-30) cc_final: 0.7474 (tp-100) REVERT: A 222 LEU cc_start: 0.8899 (tp) cc_final: 0.8662 (tp) REVERT: A 224 PHE cc_start: 0.8084 (m-10) cc_final: 0.7814 (m-10) REVERT: A 226 VAL cc_start: 0.8944 (p) cc_final: 0.8551 (p) REVERT: A 228 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7622 (ttm170) REVERT: A 231 LYS cc_start: 0.9024 (mptt) cc_final: 0.8745 (mptt) REVERT: A 255 LEU cc_start: 0.7904 (mt) cc_final: 0.7593 (mt) REVERT: A 260 ASP cc_start: 0.7792 (p0) cc_final: 0.7569 (p0) REVERT: A 272 MET cc_start: 0.8035 (mtt) cc_final: 0.7359 (mtt) REVERT: A 275 ASN cc_start: 0.8728 (m110) cc_final: 0.8093 (m110) REVERT: A 293 LYS cc_start: 0.8019 (pttm) cc_final: 0.7383 (pttm) REVERT: A 305 GLU cc_start: 0.8665 (tt0) cc_final: 0.7884 (tp30) REVERT: A 316 MET cc_start: 0.6755 (tmm) cc_final: 0.6259 (tmm) REVERT: A 320 HIS cc_start: 0.7412 (t-90) cc_final: 0.6764 (t-170) REVERT: A 324 THR cc_start: 0.8141 (t) cc_final: 0.7871 (p) REVERT: A 328 LEU cc_start: 0.8155 (mt) cc_final: 0.7935 (mt) REVERT: A 330 THR cc_start: 0.8919 (m) cc_final: 0.8597 (p) REVERT: A 346 GLU cc_start: 0.7832 (mp0) cc_final: 0.7525 (mp0) REVERT: A 351 LYS cc_start: 0.8575 (tttp) cc_final: 0.7752 (mmtm) REVERT: A 355 ARG cc_start: 0.8475 (ttm110) cc_final: 0.7783 (ttm110) REVERT: A 368 LYS cc_start: 0.8816 (mtpt) cc_final: 0.8476 (mtpt) REVERT: A 369 ARG cc_start: 0.9147 (ptm-80) cc_final: 0.8730 (ptm-80) REVERT: A 370 LEU cc_start: 0.8989 (tt) cc_final: 0.8501 (tt) REVERT: A 382 HIS cc_start: 0.7500 (t-90) cc_final: 0.7141 (t-90) REVERT: A 406 TRP cc_start: 0.8785 (t60) cc_final: 0.8051 (t60) REVERT: A 409 TYR cc_start: 0.8659 (t80) cc_final: 0.8213 (t80) REVERT: A 426 TYR cc_start: 0.7036 (p90) cc_final: 0.6760 (p90) REVERT: A 441 THR cc_start: 0.6914 (t) cc_final: 0.6514 (m) REVERT: A 482 LYS cc_start: 0.7787 (mmmm) cc_final: 0.7187 (mmmm) REVERT: A 489 ASN cc_start: 0.6916 (p0) cc_final: 0.6697 (p0) REVERT: A 502 LEU cc_start: 0.9052 (pp) cc_final: 0.8586 (pp) REVERT: A 505 LYS cc_start: 0.9221 (tmtt) cc_final: 0.8897 (tmtt) REVERT: A 516 VAL cc_start: 0.8803 (m) cc_final: 0.8337 (p) REVERT: A 520 ASN cc_start: 0.8851 (m-40) cc_final: 0.8516 (m-40) REVERT: A 525 ASN cc_start: 0.6779 (m-40) cc_final: 0.6174 (m-40) REVERT: A 565 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7532 (mt-10) REVERT: A 569 ASN cc_start: 0.7220 (m110) cc_final: 0.6926 (m110) REVERT: B 72 GLN cc_start: 0.7179 (mm110) cc_final: 0.6595 (mm110) REVERT: B 106 CYS cc_start: 0.7567 (t) cc_final: 0.6750 (m) REVERT: B 128 LYS cc_start: 0.8458 (tttm) cc_final: 0.8017 (tttm) REVERT: B 136 LYS cc_start: 0.7914 (mptt) cc_final: 0.7234 (mptt) REVERT: B 143 ASN cc_start: 0.8224 (p0) cc_final: 0.7865 (p0) REVERT: C 30 LYS cc_start: 0.8178 (mttt) cc_final: 0.7923 (mttt) REVERT: C 32 LEU cc_start: 0.7955 (mt) cc_final: 0.7639 (mt) REVERT: C 41 TYR cc_start: 0.7174 (p90) cc_final: 0.6847 (p90) REVERT: C 53 LYS cc_start: 0.6954 (mppt) cc_final: 0.6339 (mppt) REVERT: C 62 MET cc_start: 0.6430 (tpt) cc_final: 0.6099 (tpt) REVERT: C 71 ASN cc_start: 0.7701 (m110) cc_final: 0.7411 (m110) REVERT: C 84 GLN cc_start: 0.7898 (mp10) cc_final: 0.7377 (mp10) REVERT: C 95 LYS cc_start: 0.9115 (mppt) cc_final: 0.8712 (mppt) REVERT: C 98 MET cc_start: 0.7462 (ttm) cc_final: 0.7117 (ttm) REVERT: C 139 LYS cc_start: 0.7635 (tmmt) cc_final: 0.7273 (ptmm) REVERT: C 144 GLU cc_start: 0.7172 (tp30) cc_final: 0.6642 (tm-30) REVERT: C 159 ASP cc_start: 0.7567 (t0) cc_final: 0.7047 (t0) REVERT: C 164 MET cc_start: 0.8556 (ppp) cc_final: 0.8228 (ppp) REVERT: C 199 TYR cc_start: 0.7894 (t80) cc_final: 0.7615 (t80) REVERT: C 204 TYR cc_start: 0.7812 (m-80) cc_final: 0.7442 (m-10) REVERT: C 218 GLN cc_start: 0.7482 (mt0) cc_final: 0.6952 (mt0) REVERT: C 225 CYS cc_start: 0.8577 (m) cc_final: 0.8353 (m) REVERT: C 236 LYS cc_start: 0.8758 (mppt) cc_final: 0.8223 (mppt) REVERT: C 264 VAL cc_start: 0.7936 (m) cc_final: 0.7652 (p) REVERT: C 273 PHE cc_start: 0.8215 (m-10) cc_final: 0.7882 (m-10) REVERT: C 292 GLU cc_start: 0.8714 (pm20) cc_final: 0.8369 (pm20) REVERT: C 305 GLU cc_start: 0.8016 (tp30) cc_final: 0.7729 (tp30) REVERT: C 306 MET cc_start: 0.8108 (tmm) cc_final: 0.7696 (tmm) REVERT: C 316 MET cc_start: 0.7391 (mtt) cc_final: 0.7183 (mtt) REVERT: C 323 GLN cc_start: 0.8775 (mt0) cc_final: 0.8486 (mm-40) REVERT: C 351 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8747 (tttm) REVERT: C 365 ASP cc_start: 0.7945 (p0) cc_final: 0.7691 (p0) REVERT: C 369 ARG cc_start: 0.8445 (mmp-170) cc_final: 0.8223 (mmp-170) REVERT: C 410 GLU cc_start: 0.8295 (tt0) cc_final: 0.7915 (tt0) REVERT: C 445 LYS cc_start: 0.8343 (mttm) cc_final: 0.7904 (mttm) REVERT: C 464 GLU cc_start: 0.6914 (mp0) cc_final: 0.6643 (mp0) REVERT: C 465 GLU cc_start: 0.7084 (tp30) cc_final: 0.6818 (tp30) REVERT: C 476 PHE cc_start: 0.8010 (m-80) cc_final: 0.7688 (m-80) REVERT: C 504 GLU cc_start: 0.8482 (tp30) cc_final: 0.8006 (tp30) REVERT: C 536 LYS cc_start: 0.7937 (ttmt) cc_final: 0.7501 (ttmt) REVERT: C 549 TYR cc_start: 0.7568 (m-80) cc_final: 0.7360 (m-80) REVERT: C 550 LYS cc_start: 0.8395 (mttt) cc_final: 0.8180 (mttt) REVERT: C 555 LEU cc_start: 0.8309 (mm) cc_final: 0.8018 (mm) REVERT: C 557 LEU cc_start: 0.8983 (mm) cc_final: 0.8766 (mm) REVERT: C 566 LYS cc_start: 0.8733 (pttp) cc_final: 0.8365 (pttp) REVERT: C 584 HIS cc_start: 0.8516 (m90) cc_final: 0.8254 (m90) REVERT: C 603 MET cc_start: 0.7662 (mtt) cc_final: 0.7372 (mtt) REVERT: C 606 LEU cc_start: 0.8741 (mp) cc_final: 0.8489 (mp) REVERT: D 32 ASN cc_start: 0.9082 (t0) cc_final: 0.8878 (t0) REVERT: D 78 ASN cc_start: 0.8947 (t0) cc_final: 0.8551 (t0) REVERT: D 103 HIS cc_start: 0.6836 (m-70) cc_final: 0.6545 (m-70) outliers start: 0 outliers final: 0 residues processed: 442 average time/residue: 0.2843 time to fit residues: 176.0488 Evaluate side-chains 408 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 140 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 157 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 7 optimal weight: 0.0170 chunk 108 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN A 343 HIS A 459 GLN ** C 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 HIS ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.156294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122186 restraints weight = 30350.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126520 restraints weight = 17721.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.129464 restraints weight = 11640.264| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14205 Z= 0.145 Angle : 0.738 12.880 19562 Z= 0.383 Chirality : 0.043 0.175 2195 Planarity : 0.005 0.057 2244 Dihedral : 21.064 169.853 2554 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.47 % Favored : 91.47 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.21), residues: 1535 helix: 0.12 (0.21), residues: 591 sheet: -0.64 (0.34), residues: 242 loop : -1.60 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 259 HIS 0.016 0.001 HIS A 229 PHE 0.031 0.001 PHE A 589 TYR 0.020 0.001 TYR A 595 ARG 0.014 0.001 ARG C 149 Details of bonding type rmsd hydrogen bonds : bond 0.04171 ( 580) hydrogen bonds : angle 5.09218 ( 1605) covalent geometry : bond 0.00316 (14204) covalent geometry : angle 0.73767 (19562) Misc. bond : bond 0.00091 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5431.03 seconds wall clock time: 94 minutes 29.88 seconds (5669.88 seconds total)