Starting phenix.real_space_refine on Sun Nov 17 04:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/11_2024/8ona_16984.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/11_2024/8ona_16984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/11_2024/8ona_16984.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/11_2024/8ona_16984.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/11_2024/8ona_16984.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ona_16984/11_2024/8ona_16984.cif" } resolution = 3.0 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= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8217 2.51 5 N 2154 2.21 5 O 2421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12900 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4188 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 29, 'TRANS': 493} Chain breaks: 1 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 41 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Restraints were copied for chains: C, B, D, F Time building chain proxies: 8.08, per 1000 atoms: 0.63 Number of scatterers: 12900 At special positions: 0 Unit cell: (107.31, 104.244, 133.882, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2421 8.00 N 2154 7.00 C 8217 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 80 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 172 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 405 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 401 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 381 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 350 " distance=2.03 Simple disulfide: pdb=" SG CYS A 360 " - pdb=" SG CYS A 368 " distance=2.03 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=3, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 180 " " NAG A 602 " - " ASN A 299 " " NAG A 603 " - " ASN A 392 " " NAG A 604 " - " ASN A 444 " " NAG A 605 " - " ASN A 460 " " NAG B 601 " - " ASN B 180 " " NAG B 602 " - " ASN B 299 " " NAG B 603 " - " ASN B 392 " " NAG B 604 " - " ASN B 444 " " NAG B 605 " - " ASN B 460 " " NAG C 601 " - " ASN C 180 " " NAG C 602 " - " ASN C 299 " " NAG C 603 " - " ASN C 392 " " NAG C 604 " - " ASN C 444 " " NAG C 605 " - " ASN C 460 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.43 Conformation dependent library (CDL) restraints added in 1.5 seconds 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2988 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 9 sheets defined 49.6% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 17 through 24 removed outlier: 4.449A pdb=" N LYS A 21 " --> pdb=" O HIS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 58 Processing helix chain 'A' and resid 86 through 100 Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.546A pdb=" N ILE A 107 " --> pdb=" O PHE A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 removed outlier: 3.663A pdb=" N LYS A 124 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 136 through 144 Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.675A pdb=" N PHE A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.657A pdb=" N CYS A 318 " --> pdb=" O ARG A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 362 Processing helix chain 'A' and resid 365 through 390 removed outlier: 4.224A pdb=" N THR A 390 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 423 through 435 Processing helix chain 'A' and resid 438 through 444 removed outlier: 3.665A pdb=" N PHE A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'A' and resid 493 through 509 Processing helix chain 'A' and resid 512 through 529 Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 17 through 24 removed outlier: 4.450A pdb=" N LYS B 21 " --> pdb=" O HIS B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 58 Processing helix chain 'B' and resid 86 through 100 Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.546A pdb=" N ILE B 107 " --> pdb=" O PHE B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 124 removed outlier: 3.663A pdb=" N LYS B 124 " --> pdb=" O LYS B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 136 through 144 Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.676A pdb=" N PHE B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 314 through 332 removed outlier: 3.658A pdb=" N CYS B 318 " --> pdb=" O ARG B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 365 through 390 removed outlier: 4.224A pdb=" N THR B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 398 Processing helix chain 'B' and resid 423 through 435 Processing helix chain 'B' and resid 438 through 444 removed outlier: 3.665A pdb=" N PHE B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 493 through 509 Processing helix chain 'B' and resid 512 through 529 Processing helix chain 'C' and resid 3 through 14 Processing helix chain 'C' and resid 17 through 24 removed outlier: 4.450A pdb=" N LYS C 21 " --> pdb=" O HIS C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 58 Processing helix chain 'C' and resid 86 through 100 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.546A pdb=" N ILE C 107 " --> pdb=" O PHE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 removed outlier: 3.663A pdb=" N LYS C 124 " --> pdb=" O LYS C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 145 through 153 removed outlier: 3.675A pdb=" N PHE C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 314 through 332 removed outlier: 3.657A pdb=" N CYS C 318 " --> pdb=" O ARG C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 Processing helix chain 'C' and resid 365 through 390 removed outlier: 4.224A pdb=" N THR C 390 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 398 Processing helix chain 'C' and resid 423 through 435 Processing helix chain 'C' and resid 438 through 444 removed outlier: 3.665A pdb=" N PHE C 443 " --> pdb=" O ASN C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 447 No H-bonds generated for 'chain 'C' and resid 445 through 447' Processing helix chain 'C' and resid 448 through 459 Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 493 through 509 Processing helix chain 'C' and resid 512 through 529 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.455A pdb=" N ILE A 222 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N CYS A 172 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER A 220 " --> pdb=" O CYS A 172 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR A 174 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A 218 " --> pdb=" O TYR A 174 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE A 279 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.458A pdb=" N ASN A 195 " --> pdb=" O ASN A 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN A 81 " --> pdb=" O ASN A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 61 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.455A pdb=" N ILE B 222 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS B 172 " --> pdb=" O SER B 220 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 220 " --> pdb=" O CYS B 172 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N TYR B 174 " --> pdb=" O GLY B 218 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY B 218 " --> pdb=" O TYR B 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE B 279 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.457A pdb=" N ASN B 195 " --> pdb=" O ASN B 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN B 81 " --> pdb=" O ASN B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 61 through 68 Processing sheet with id=AA8, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.454A pdb=" N ILE C 222 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N CYS C 172 " --> pdb=" O SER C 220 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER C 220 " --> pdb=" O CYS C 172 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N TYR C 174 " --> pdb=" O GLY C 218 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY C 218 " --> pdb=" O TYR C 174 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE C 279 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 185 through 189 removed outlier: 6.458A pdb=" N ASN C 195 " --> pdb=" O ASN C 81 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ASN C 81 " --> pdb=" O ASN C 195 " (cutoff:3.500A) 670 hydrogen bonds defined for protein. 1893 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.02 Time building geometry restraints manager: 3.79 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: 3176 1.33 - 1.45: 2854 1.45 - 1.58: 7035 1.58 - 1.70: 0 1.70 - 1.82: 162 Bond restraints: 13227 Sorted by residual: bond pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 1.456 1.504 -0.048 1.18e-02 7.18e+03 1.65e+01 bond pdb=" N GLN C 13 " pdb=" CA GLN C 13 " ideal model delta sigma weight residual 1.456 1.503 -0.048 1.18e-02 7.18e+03 1.62e+01 bond pdb=" N GLN A 13 " pdb=" CA GLN A 13 " ideal model delta sigma weight residual 1.456 1.503 -0.047 1.18e-02 7.18e+03 1.61e+01 bond pdb=" C ASP A 5 " pdb=" O ASP A 5 " ideal model delta sigma weight residual 1.235 1.277 -0.042 1.26e-02 6.30e+03 1.10e+01 bond pdb=" C ASP B 5 " pdb=" O ASP B 5 " ideal model delta sigma weight residual 1.235 1.277 -0.041 1.26e-02 6.30e+03 1.07e+01 ... (remaining 13222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17275 1.81 - 3.61: 529 3.61 - 5.42: 85 5.42 - 7.23: 15 7.23 - 9.04: 6 Bond angle restraints: 17910 Sorted by residual: angle pdb=" C GLU C 12 " pdb=" N GLN C 13 " pdb=" CA GLN C 13 " ideal model delta sigma weight residual 122.73 113.82 8.91 1.61e+00 3.86e-01 3.06e+01 angle pdb=" C GLU B 12 " pdb=" N GLN B 13 " pdb=" CA GLN B 13 " ideal model delta sigma weight residual 122.73 113.83 8.90 1.61e+00 3.86e-01 3.05e+01 angle pdb=" C GLU A 12 " pdb=" N GLN A 13 " pdb=" CA GLN A 13 " ideal model delta sigma weight residual 122.73 113.86 8.87 1.61e+00 3.86e-01 3.03e+01 angle pdb=" C GLN C 13 " pdb=" N THR C 14 " pdb=" CA THR C 14 " ideal model delta sigma weight residual 122.64 113.60 9.04 1.70e+00 3.46e-01 2.83e+01 angle pdb=" C GLN A 13 " pdb=" N THR A 14 " pdb=" CA THR A 14 " ideal model delta sigma weight residual 122.64 113.62 9.02 1.70e+00 3.46e-01 2.81e+01 ... (remaining 17905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 7245 15.80 - 31.59: 680 31.59 - 47.39: 148 47.39 - 63.18: 27 63.18 - 78.98: 21 Dihedral angle restraints: 8121 sinusoidal: 3492 harmonic: 4629 Sorted by residual: dihedral pdb=" CA MET A 16 " pdb=" C MET A 16 " pdb=" N HIS A 17 " pdb=" CA HIS A 17 " ideal model delta harmonic sigma weight residual -180.00 -160.21 -19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET B 16 " pdb=" C MET B 16 " pdb=" N HIS B 17 " pdb=" CA HIS B 17 " ideal model delta harmonic sigma weight residual -180.00 -160.22 -19.78 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA MET C 16 " pdb=" C MET C 16 " pdb=" N HIS C 17 " pdb=" CA HIS C 17 " ideal model delta harmonic sigma weight residual 180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 8118 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1733 0.081 - 0.162: 199 0.162 - 0.243: 9 0.243 - 0.324: 3 0.324 - 0.404: 6 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CA ARG C 102 " pdb=" N ARG C 102 " pdb=" C ARG C 102 " pdb=" CB ARG C 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA ARG A 102 " pdb=" N ARG A 102 " pdb=" C ARG A 102 " pdb=" CB ARG A 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ARG B 102 " pdb=" N ARG B 102 " pdb=" C ARG B 102 " pdb=" CB ARG B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 ... (remaining 1947 not shown) Planarity restraints: 2322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 248 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.30e+00 pdb=" C ALA C 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA C 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL C 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 248 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C ALA A 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA A 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL A 249 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 248 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.19e+00 pdb=" C ALA B 248 " 0.050 2.00e-02 2.50e+03 pdb=" O ALA B 248 " -0.019 2.00e-02 2.50e+03 pdb=" N VAL B 249 " -0.017 2.00e-02 2.50e+03 ... (remaining 2319 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 86 2.60 - 3.18: 11419 3.18 - 3.75: 19465 3.75 - 4.33: 28137 4.33 - 4.90: 46431 Nonbonded interactions: 105538 Sorted by model distance: nonbonded pdb=" SG CYS C 322 " pdb=" SG CYS C 399 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 80 " pdb=" SG CYS B 196 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS C 80 " pdb=" SG CYS C 196 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 322 " pdb=" SG CYS B 399 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 333 " pdb=" SG CYS B 350 " model vdw 2.030 3.760 ... (remaining 105533 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.020 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:13.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.004 0.051 13227 Z= 0.296 Angle : 0.738 9.037 17910 Z= 0.435 Chirality : 0.052 0.404 1950 Planarity : 0.004 0.029 2307 Dihedral : 13.104 78.976 5109 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.43 % Allowed : 7.49 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.21), residues: 1563 helix: 0.16 (0.19), residues: 684 sheet: 1.09 (0.30), residues: 279 loop : 0.59 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 34 HIS 0.005 0.001 HIS B 376 PHE 0.024 0.001 PHE A 33 TYR 0.014 0.002 TYR B 414 ARG 0.003 0.000 ARG B 102 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 493 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.7599 (ttt) cc_final: 0.7225 (ttt) REVERT: A 49 MET cc_start: 0.6342 (ttt) cc_final: 0.6038 (ttp) REVERT: A 61 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7667 (ttmm) REVERT: A 100 ASP cc_start: 0.7278 (t0) cc_final: 0.6722 (t0) REVERT: A 111 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7675 (mt-10) REVERT: A 120 LYS cc_start: 0.7799 (mttt) cc_final: 0.7550 (tppp) REVERT: A 138 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 203 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7346 (mm-30) REVERT: A 232 LYS cc_start: 0.8380 (mttt) cc_final: 0.8086 (mttm) REVERT: A 271 GLU cc_start: 0.7437 (pt0) cc_final: 0.7225 (pt0) REVERT: A 288 ARG cc_start: 0.7311 (mtp85) cc_final: 0.6768 (mtm-85) REVERT: A 290 ASN cc_start: 0.7792 (m110) cc_final: 0.7591 (m-40) REVERT: A 302 ASP cc_start: 0.7303 (p0) cc_final: 0.6937 (p0) REVERT: A 303 LYS cc_start: 0.7634 (mtmt) cc_final: 0.7370 (mtmt) REVERT: A 380 LYS cc_start: 0.6968 (mtpt) cc_final: 0.6720 (mtpt) REVERT: A 388 LYS cc_start: 0.7247 (mtpp) cc_final: 0.7018 (mtpp) REVERT: A 409 SER cc_start: 0.7501 (m) cc_final: 0.7062 (t) REVERT: A 411 ASP cc_start: 0.7684 (m-30) cc_final: 0.7285 (m-30) REVERT: A 438 LYS cc_start: 0.8094 (mttt) cc_final: 0.7818 (mttp) REVERT: A 440 ASN cc_start: 0.7226 (p0) cc_final: 0.6602 (t0) REVERT: A 465 GLU cc_start: 0.7711 (tp30) cc_final: 0.7496 (tp30) REVERT: A 470 ASP cc_start: 0.7746 (m-30) cc_final: 0.7252 (m-30) REVERT: B 10 PHE cc_start: 0.6376 (t80) cc_final: 0.6023 (t80) REVERT: B 21 LYS cc_start: 0.7265 (tppp) cc_final: 0.6955 (mmtt) REVERT: B 33 PHE cc_start: 0.7398 (t80) cc_final: 0.7149 (t80) REVERT: B 44 MET cc_start: 0.7439 (ttt) cc_final: 0.6852 (ttt) REVERT: B 60 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7633 (Cg_exo) REVERT: B 61 LYS cc_start: 0.8018 (ttmt) cc_final: 0.7513 (mtpp) REVERT: B 62 LYS cc_start: 0.6305 (ttpp) cc_final: 0.6079 (tttp) REVERT: B 100 ASP cc_start: 0.7176 (t0) cc_final: 0.6607 (t70) REVERT: B 135 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 138 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7296 (mp0) REVERT: B 141 GLN cc_start: 0.8124 (mm110) cc_final: 0.7877 (mm110) REVERT: B 156 GLU cc_start: 0.7726 (tt0) cc_final: 0.7498 (tt0) REVERT: B 171 ASN cc_start: 0.8276 (t0) cc_final: 0.8056 (m-40) REVERT: B 203 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7255 (mm-30) REVERT: B 232 LYS cc_start: 0.8211 (mttt) cc_final: 0.7902 (mttp) REVERT: B 244 GLU cc_start: 0.7871 (tp30) cc_final: 0.7668 (tp30) REVERT: B 288 ARG cc_start: 0.7142 (mtp85) cc_final: 0.6751 (mtm110) REVERT: B 301 SER cc_start: 0.6940 (t) cc_final: 0.6600 (p) REVERT: B 303 LYS cc_start: 0.7801 (mtmt) cc_final: 0.7312 (mtpp) REVERT: B 308 ASP cc_start: 0.7746 (m-30) cc_final: 0.7514 (p0) REVERT: B 310 THR cc_start: 0.8384 (p) cc_final: 0.7780 (t) REVERT: B 311 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6481 (mm-30) REVERT: B 329 GLU cc_start: 0.7453 (tt0) cc_final: 0.7140 (tt0) REVERT: B 353 ASP cc_start: 0.7528 (p0) cc_final: 0.7230 (p0) REVERT: B 380 LYS cc_start: 0.7046 (mtpt) cc_final: 0.6841 (mtpt) REVERT: B 402 PHE cc_start: 0.7967 (m-80) cc_final: 0.7636 (m-80) REVERT: B 425 GLU cc_start: 0.7451 (tp30) cc_final: 0.7138 (mm-30) REVERT: B 440 ASN cc_start: 0.7348 (p0) cc_final: 0.7120 (m-40) REVERT: B 462 SER cc_start: 0.8231 (m) cc_final: 0.7773 (p) REVERT: B 465 GLU cc_start: 0.7664 (tp30) cc_final: 0.7462 (tp30) REVERT: B 466 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7040 (mm-30) REVERT: B 492 TYR cc_start: 0.7852 (t80) cc_final: 0.7159 (t80) REVERT: B 518 GLU cc_start: 0.7175 (tp30) cc_final: 0.6958 (tp30) REVERT: C 7 MET cc_start: 0.6814 (ttm) cc_final: 0.6596 (ttm) REVERT: C 10 PHE cc_start: 0.6183 (t80) cc_final: 0.5851 (t80) REVERT: C 33 PHE cc_start: 0.7353 (t80) cc_final: 0.7052 (t80) REVERT: C 61 LYS cc_start: 0.7886 (ttmt) cc_final: 0.7547 (ttmm) REVERT: C 66 GLU cc_start: 0.7472 (pt0) cc_final: 0.6812 (pm20) REVERT: C 99 GLU cc_start: 0.7502 (tt0) cc_final: 0.7237 (tt0) REVERT: C 100 ASP cc_start: 0.7379 (t0) cc_final: 0.6845 (t70) REVERT: C 120 LYS cc_start: 0.7695 (mttt) cc_final: 0.7408 (ttmm) REVERT: C 138 GLU cc_start: 0.7714 (mt-10) cc_final: 0.7464 (mp0) REVERT: C 142 GLU cc_start: 0.7499 (tt0) cc_final: 0.7223 (tt0) REVERT: C 156 GLU cc_start: 0.7688 (tt0) cc_final: 0.7267 (pm20) REVERT: C 178 ARG cc_start: 0.7384 (ttm170) cc_final: 0.7000 (ttp-170) REVERT: C 181 LYS cc_start: 0.7705 (mtmm) cc_final: 0.7236 (mtpp) REVERT: C 232 LYS cc_start: 0.8394 (mttt) cc_final: 0.8033 (mttp) REVERT: C 249 VAL cc_start: 0.8242 (m) cc_final: 0.8012 (m) REVERT: C 288 ARG cc_start: 0.7201 (mtp85) cc_final: 0.6772 (mtm110) REVERT: C 303 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7369 (mtmt) REVERT: C 346 ASN cc_start: 0.7610 (m-40) cc_final: 0.7362 (m-40) REVERT: C 441 GLU cc_start: 0.7263 (mt-10) cc_final: 0.7062 (mm-30) REVERT: C 462 SER cc_start: 0.8179 (m) cc_final: 0.7817 (t) REVERT: C 463 ASN cc_start: 0.7933 (t0) cc_final: 0.7243 (t0) REVERT: C 465 GLU cc_start: 0.7788 (tp30) cc_final: 0.7518 (tp30) REVERT: C 466 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7265 (mm-30) REVERT: C 470 ASP cc_start: 0.7767 (m-30) cc_final: 0.7556 (m-30) REVERT: C 480 ASP cc_start: 0.7265 (m-30) cc_final: 0.6881 (m-30) REVERT: C 487 GLN cc_start: 0.7708 (tt0) cc_final: 0.7374 (tt0) REVERT: C 492 TYR cc_start: 0.7659 (t80) cc_final: 0.6990 (t80) REVERT: C 494 ARG cc_start: 0.6765 (ttp-110) cc_final: 0.6553 (ttp-110) outliers start: 6 outliers final: 0 residues processed: 496 average time/residue: 1.4643 time to fit residues: 781.8706 Evaluate side-chains 396 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 0.7980 chunk 141 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 ASN A 297 HIS A 495 ASN B 48 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN C 48 GLN C 91 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 ASN C 297 HIS C 319 GLN ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN C 496 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 13227 Z= 0.292 Angle : 0.635 7.214 17910 Z= 0.330 Chirality : 0.046 0.259 1950 Planarity : 0.005 0.040 2307 Dihedral : 5.137 30.280 2040 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.43 % Allowed : 13.92 % Favored : 83.65 % 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: 1.11 (0.21), residues: 1563 helix: 0.94 (0.20), residues: 690 sheet: 0.90 (0.28), residues: 279 loop : 0.64 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 349 HIS 0.005 0.001 HIS B 243 PHE 0.022 0.002 PHE B 431 TYR 0.014 0.002 TYR C 118 ARG 0.004 0.001 ARG C 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 402 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.7483 (ttp) cc_final: 0.7047 (ptp) REVERT: A 44 MET cc_start: 0.7573 (ttt) cc_final: 0.7174 (ttt) REVERT: A 49 MET cc_start: 0.6356 (ttt) cc_final: 0.6067 (ttp) REVERT: A 61 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7696 (ttmm) REVERT: A 62 LYS cc_start: 0.6567 (ttpp) cc_final: 0.6350 (tttp) REVERT: A 203 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7386 (mm-30) REVERT: A 213 GLU cc_start: 0.7113 (pt0) cc_final: 0.6896 (pt0) REVERT: A 232 LYS cc_start: 0.8442 (mttt) cc_final: 0.8170 (mttm) REVERT: A 288 ARG cc_start: 0.7498 (mtp85) cc_final: 0.7103 (mtm-85) REVERT: A 301 SER cc_start: 0.7383 (t) cc_final: 0.6668 (p) REVERT: A 302 ASP cc_start: 0.7289 (p0) cc_final: 0.6970 (p0) REVERT: A 336 VAL cc_start: 0.7865 (p) cc_final: 0.7580 (t) REVERT: A 380 LYS cc_start: 0.6905 (mtpt) cc_final: 0.6685 (mtpt) REVERT: A 407 GLU cc_start: 0.7442 (tt0) cc_final: 0.7147 (tt0) REVERT: A 438 LYS cc_start: 0.7893 (mttt) cc_final: 0.7635 (mttm) REVERT: A 440 ASN cc_start: 0.7288 (p0) cc_final: 0.6778 (t0) REVERT: A 465 GLU cc_start: 0.7686 (tp30) cc_final: 0.7334 (tp30) REVERT: A 466 GLU cc_start: 0.7656 (mm-30) cc_final: 0.7356 (mm-30) REVERT: A 470 ASP cc_start: 0.7897 (m-30) cc_final: 0.7445 (m-30) REVERT: A 521 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7404 (tm-30) REVERT: B 15 THR cc_start: 0.7531 (p) cc_final: 0.7219 (p) REVERT: B 33 PHE cc_start: 0.7416 (t80) cc_final: 0.7114 (t80) REVERT: B 44 MET cc_start: 0.7385 (ttt) cc_final: 0.6785 (ttt) REVERT: B 49 MET cc_start: 0.6401 (ttt) cc_final: 0.5676 (tmm) REVERT: B 51 GLU cc_start: 0.6588 (tp30) cc_final: 0.6375 (tp30) REVERT: B 61 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7575 (ttpp) REVERT: B 66 GLU cc_start: 0.7643 (pt0) cc_final: 0.7121 (pm20) REVERT: B 120 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7680 (ttmm) REVERT: B 121 LYS cc_start: 0.7791 (ttpp) cc_final: 0.7508 (tttm) REVERT: B 135 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7174 (mt-10) REVERT: B 156 GLU cc_start: 0.7759 (tt0) cc_final: 0.7355 (tt0) REVERT: B 203 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 213 GLU cc_start: 0.7237 (pt0) cc_final: 0.6832 (pt0) REVERT: B 232 LYS cc_start: 0.8210 (mttt) cc_final: 0.7874 (mttm) REVERT: B 244 GLU cc_start: 0.7797 (tp30) cc_final: 0.7331 (tp30) REVERT: B 288 ARG cc_start: 0.7462 (mtp85) cc_final: 0.7068 (mtm-85) REVERT: B 301 SER cc_start: 0.7564 (t) cc_final: 0.6885 (p) REVERT: B 303 LYS cc_start: 0.7980 (mtmt) cc_final: 0.7467 (mtpp) REVERT: B 311 GLU cc_start: 0.6837 (mm-30) cc_final: 0.6603 (mm-30) REVERT: B 329 GLU cc_start: 0.7471 (tt0) cc_final: 0.7212 (tt0) REVERT: B 370 GLN cc_start: 0.7256 (mt0) cc_final: 0.6765 (mm110) REVERT: B 380 LYS cc_start: 0.7156 (mtpt) cc_final: 0.6855 (mtpm) REVERT: B 441 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: B 465 GLU cc_start: 0.7757 (tp30) cc_final: 0.7520 (tp30) REVERT: B 466 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7079 (mm-30) REVERT: B 492 TYR cc_start: 0.8047 (t80) cc_final: 0.7249 (t80) REVERT: B 518 GLU cc_start: 0.7224 (tp30) cc_final: 0.7003 (tp30) REVERT: B 521 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 7 MET cc_start: 0.6927 (ttm) cc_final: 0.6701 (ttm) REVERT: C 16 MET cc_start: 0.7391 (ttp) cc_final: 0.6900 (ptp) REVERT: C 33 PHE cc_start: 0.7360 (t80) cc_final: 0.6989 (t80) REVERT: C 44 MET cc_start: 0.7450 (ttt) cc_final: 0.7189 (ttt) REVERT: C 51 GLU cc_start: 0.6852 (tp30) cc_final: 0.6531 (tm-30) REVERT: C 61 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7325 (ttmm) REVERT: C 66 GLU cc_start: 0.7510 (pt0) cc_final: 0.7281 (pt0) REVERT: C 99 GLU cc_start: 0.7487 (tt0) cc_final: 0.7240 (tt0) REVERT: C 120 LYS cc_start: 0.7699 (mttt) cc_final: 0.7467 (ttmm) REVERT: C 142 GLU cc_start: 0.7654 (tt0) cc_final: 0.7420 (tt0) REVERT: C 156 GLU cc_start: 0.7742 (tt0) cc_final: 0.7372 (tt0) REVERT: C 232 LYS cc_start: 0.8406 (mttt) cc_final: 0.8050 (mttp) REVERT: C 234 ASP cc_start: 0.8071 (m-30) cc_final: 0.7832 (p0) REVERT: C 288 ARG cc_start: 0.7499 (mtp85) cc_final: 0.6989 (mtm-85) REVERT: C 301 SER cc_start: 0.7590 (t) cc_final: 0.6950 (p) REVERT: C 312 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.7775 (ttp-170) REVERT: C 346 ASN cc_start: 0.7648 (m-40) cc_final: 0.7379 (m-40) REVERT: C 370 GLN cc_start: 0.7266 (mt0) cc_final: 0.6705 (mm110) REVERT: C 438 LYS cc_start: 0.7869 (mttt) cc_final: 0.7551 (mttt) REVERT: C 462 SER cc_start: 0.8272 (m) cc_final: 0.7888 (t) REVERT: C 463 ASN cc_start: 0.8014 (t0) cc_final: 0.7250 (t0) REVERT: C 465 GLU cc_start: 0.7853 (tp30) cc_final: 0.7555 (tp30) REVERT: C 466 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7244 (mm-30) REVERT: C 488 GLU cc_start: 0.7419 (mt-10) cc_final: 0.7136 (mt-10) REVERT: C 492 TYR cc_start: 0.7805 (t80) cc_final: 0.7430 (t80) REVERT: C 494 ARG cc_start: 0.6818 (ttp-110) cc_final: 0.6582 (ttp-110) REVERT: C 521 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7267 (tm-30) outliers start: 34 outliers final: 14 residues processed: 422 average time/residue: 1.4592 time to fit residues: 662.7788 Evaluate side-chains 396 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 380 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 270 THR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 391 LYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 363 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 141 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 HIS B 297 HIS ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 482 ASN C 13 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13227 Z= 0.227 Angle : 0.580 9.643 17910 Z= 0.298 Chirality : 0.044 0.264 1950 Planarity : 0.005 0.046 2307 Dihedral : 4.873 33.464 2040 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.50 % Allowed : 16.70 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1563 helix: 1.41 (0.20), residues: 690 sheet: 0.79 (0.28), residues: 279 loop : 0.56 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 349 HIS 0.005 0.001 HIS A 297 PHE 0.024 0.002 PHE A 33 TYR 0.014 0.001 TYR B 118 ARG 0.005 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 394 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7426 (tptp) REVERT: A 44 MET cc_start: 0.7448 (ttt) cc_final: 0.7052 (ttt) REVERT: A 49 MET cc_start: 0.6289 (ttt) cc_final: 0.5875 (tmm) REVERT: A 61 LYS cc_start: 0.7969 (ttmt) cc_final: 0.7644 (ttmm) REVERT: A 62 LYS cc_start: 0.6572 (ttpp) cc_final: 0.6363 (tttp) REVERT: A 102 ARG cc_start: 0.7233 (mtm-85) cc_final: 0.6889 (mtm-85) REVERT: A 178 ARG cc_start: 0.7439 (ttm170) cc_final: 0.7148 (mtm-85) REVERT: A 203 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 213 GLU cc_start: 0.7098 (pt0) cc_final: 0.6652 (pt0) REVERT: A 232 LYS cc_start: 0.8453 (mttt) cc_final: 0.8123 (mttm) REVERT: A 288 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7161 (mtm-85) REVERT: A 293 ILE cc_start: 0.6519 (OUTLIER) cc_final: 0.5564 (mm) REVERT: A 301 SER cc_start: 0.7476 (t) cc_final: 0.6948 (p) REVERT: A 302 ASP cc_start: 0.7310 (p0) cc_final: 0.7008 (p0) REVERT: A 336 VAL cc_start: 0.7905 (p) cc_final: 0.7675 (t) REVERT: A 380 LYS cc_start: 0.6650 (mtpt) cc_final: 0.6281 (mttp) REVERT: A 409 SER cc_start: 0.8062 (m) cc_final: 0.7682 (t) REVERT: A 438 LYS cc_start: 0.7859 (mttt) cc_final: 0.7617 (mttm) REVERT: A 440 ASN cc_start: 0.7166 (p0) cc_final: 0.6763 (t0) REVERT: A 465 GLU cc_start: 0.7732 (tp30) cc_final: 0.7399 (tp30) REVERT: A 466 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 470 ASP cc_start: 0.7899 (m-30) cc_final: 0.7425 (m-30) REVERT: A 521 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 16 MET cc_start: 0.7319 (OUTLIER) cc_final: 0.6884 (ptp) REVERT: B 33 PHE cc_start: 0.7406 (t80) cc_final: 0.7091 (t80) REVERT: B 44 MET cc_start: 0.7342 (ttt) cc_final: 0.6757 (ttt) REVERT: B 49 MET cc_start: 0.6381 (ttt) cc_final: 0.5700 (tmm) REVERT: B 51 GLU cc_start: 0.6617 (tp30) cc_final: 0.6387 (tp30) REVERT: B 61 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7665 (ttpp) REVERT: B 120 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7658 (ttmm) REVERT: B 121 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7486 (tttm) REVERT: B 135 GLU cc_start: 0.7381 (mt-10) cc_final: 0.7107 (mt-10) REVERT: B 156 GLU cc_start: 0.7719 (tt0) cc_final: 0.7337 (tt0) REVERT: B 203 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7406 (mm-30) REVERT: B 232 LYS cc_start: 0.8214 (mttt) cc_final: 0.7978 (mttm) REVERT: B 244 GLU cc_start: 0.7774 (tp30) cc_final: 0.7356 (tp30) REVERT: B 288 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6982 (mtm-85) REVERT: B 301 SER cc_start: 0.7608 (t) cc_final: 0.7005 (p) REVERT: B 303 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7546 (mtpp) REVERT: B 311 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6515 (mm-30) REVERT: B 329 GLU cc_start: 0.7477 (tt0) cc_final: 0.7191 (tt0) REVERT: B 370 GLN cc_start: 0.7228 (mt0) cc_final: 0.6698 (mm110) REVERT: B 380 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6881 (mtpm) REVERT: B 402 PHE cc_start: 0.7876 (m-80) cc_final: 0.7638 (m-80) REVERT: B 441 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: B 465 GLU cc_start: 0.7799 (tp30) cc_final: 0.7564 (tp30) REVERT: B 466 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7044 (mm-30) REVERT: B 485 LYS cc_start: 0.7495 (ttpp) cc_final: 0.7210 (ttpp) REVERT: B 492 TYR cc_start: 0.8075 (t80) cc_final: 0.7397 (t80) REVERT: B 521 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 10 PHE cc_start: 0.6514 (t80) cc_final: 0.6251 (t80) REVERT: C 33 PHE cc_start: 0.7379 (t80) cc_final: 0.7016 (t80) REVERT: C 44 MET cc_start: 0.7394 (ttt) cc_final: 0.7127 (ttt) REVERT: C 61 LYS cc_start: 0.7815 (ttmt) cc_final: 0.7285 (ttmm) REVERT: C 66 GLU cc_start: 0.7634 (pt0) cc_final: 0.6866 (pm20) REVERT: C 99 GLU cc_start: 0.7469 (tt0) cc_final: 0.7230 (tt0) REVERT: C 120 LYS cc_start: 0.7707 (mttt) cc_final: 0.7485 (ttmm) REVERT: C 142 GLU cc_start: 0.7644 (tt0) cc_final: 0.7362 (tt0) REVERT: C 156 GLU cc_start: 0.7728 (tt0) cc_final: 0.7180 (pm20) REVERT: C 203 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7112 (mm-30) REVERT: C 232 LYS cc_start: 0.8418 (mttt) cc_final: 0.8046 (mttp) REVERT: C 234 ASP cc_start: 0.8070 (m-30) cc_final: 0.7837 (p0) REVERT: C 253 GLU cc_start: 0.8112 (tt0) cc_final: 0.7791 (tt0) REVERT: C 288 ARG cc_start: 0.7497 (mtp85) cc_final: 0.6966 (mtm-85) REVERT: C 301 SER cc_start: 0.7660 (t) cc_final: 0.6991 (p) REVERT: C 312 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7789 (ttp-170) REVERT: C 346 ASN cc_start: 0.7702 (m-40) cc_final: 0.7423 (m-40) REVERT: C 380 LYS cc_start: 0.7621 (mtpt) cc_final: 0.7089 (mtpp) REVERT: C 438 LYS cc_start: 0.7862 (mttt) cc_final: 0.7541 (mttt) REVERT: C 462 SER cc_start: 0.8352 (m) cc_final: 0.7949 (t) REVERT: C 463 ASN cc_start: 0.8030 (t0) cc_final: 0.7254 (t0) REVERT: C 465 GLU cc_start: 0.7808 (tp30) cc_final: 0.7556 (tp30) REVERT: C 466 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7224 (mm-30) REVERT: C 487 GLN cc_start: 0.7645 (tt0) cc_final: 0.7384 (tt0) REVERT: C 488 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7188 (mt-10) REVERT: C 492 TYR cc_start: 0.7864 (t80) cc_final: 0.7492 (t80) REVERT: C 494 ARG cc_start: 0.6831 (ttp-110) cc_final: 0.6582 (ttp-110) REVERT: C 521 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7272 (tm-30) outliers start: 35 outliers final: 16 residues processed: 407 average time/residue: 1.5094 time to fit residues: 659.1469 Evaluate side-chains 393 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 373 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain C residue 46 CYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 501 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 73 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 67 optimal weight: 0.0570 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS B 482 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13227 Z= 0.210 Angle : 0.556 9.443 17910 Z= 0.287 Chirality : 0.043 0.257 1950 Planarity : 0.004 0.054 2307 Dihedral : 4.652 28.001 2040 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.57 % Allowed : 17.56 % Favored : 79.87 % 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: 1.53 (0.21), residues: 1563 helix: 1.61 (0.20), residues: 690 sheet: 0.93 (0.28), residues: 276 loop : 0.52 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 349 HIS 0.005 0.001 HIS B 297 PHE 0.019 0.001 PHE B 431 TYR 0.014 0.001 TYR B 118 ARG 0.003 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 383 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7925 (mmmm) cc_final: 0.7522 (tptp) REVERT: A 15 THR cc_start: 0.7715 (p) cc_final: 0.7404 (p) REVERT: A 44 MET cc_start: 0.7433 (ttt) cc_final: 0.7017 (ttt) REVERT: A 49 MET cc_start: 0.6300 (ttt) cc_final: 0.5904 (tmm) REVERT: A 61 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7588 (mtpm) REVERT: A 102 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6903 (mtm180) REVERT: A 178 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7181 (mtm-85) REVERT: A 232 LYS cc_start: 0.8507 (mttt) cc_final: 0.8164 (mttm) REVERT: A 288 ARG cc_start: 0.7452 (mtp85) cc_final: 0.6935 (mtm-85) REVERT: A 289 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6629 (ttt90) REVERT: A 302 ASP cc_start: 0.7272 (p0) cc_final: 0.7018 (p0) REVERT: A 380 LYS cc_start: 0.6506 (mtpt) cc_final: 0.6199 (mttp) REVERT: A 386 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7541 (mtmt) REVERT: A 407 GLU cc_start: 0.7427 (tt0) cc_final: 0.7175 (tt0) REVERT: A 438 LYS cc_start: 0.7875 (mttt) cc_final: 0.7650 (mtpp) REVERT: A 440 ASN cc_start: 0.7069 (p0) cc_final: 0.6719 (t0) REVERT: A 465 GLU cc_start: 0.7768 (tp30) cc_final: 0.7429 (tp30) REVERT: A 466 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 470 ASP cc_start: 0.7822 (m-30) cc_final: 0.7413 (m-30) REVERT: A 521 GLU cc_start: 0.7657 (tm-30) cc_final: 0.7272 (tm-30) REVERT: B 16 MET cc_start: 0.7355 (ttp) cc_final: 0.6868 (ptp) REVERT: B 33 PHE cc_start: 0.7400 (t80) cc_final: 0.7132 (t80) REVERT: B 44 MET cc_start: 0.7367 (ttt) cc_final: 0.6842 (ttt) REVERT: B 49 MET cc_start: 0.6326 (ttt) cc_final: 0.5645 (tmm) REVERT: B 51 GLU cc_start: 0.6642 (tp30) cc_final: 0.6410 (tp30) REVERT: B 61 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7661 (ttpp) REVERT: B 120 LYS cc_start: 0.7895 (ttmt) cc_final: 0.7658 (ttmm) REVERT: B 121 LYS cc_start: 0.7795 (ttpp) cc_final: 0.7467 (tttm) REVERT: B 156 GLU cc_start: 0.7690 (tt0) cc_final: 0.7290 (tt0) REVERT: B 178 ARG cc_start: 0.7513 (ttm170) cc_final: 0.7263 (ttm170) REVERT: B 203 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7374 (mm-30) REVERT: B 232 LYS cc_start: 0.8285 (mttt) cc_final: 0.8051 (mttm) REVERT: B 244 GLU cc_start: 0.7744 (tp30) cc_final: 0.7354 (tp30) REVERT: B 288 ARG cc_start: 0.7414 (mtp85) cc_final: 0.6994 (mtm-85) REVERT: B 301 SER cc_start: 0.7615 (t) cc_final: 0.7003 (p) REVERT: B 303 LYS cc_start: 0.8053 (mtmt) cc_final: 0.7455 (mtpp) REVERT: B 311 GLU cc_start: 0.6738 (mm-30) cc_final: 0.6509 (mm-30) REVERT: B 313 TYR cc_start: 0.8387 (t80) cc_final: 0.8181 (t80) REVERT: B 329 GLU cc_start: 0.7481 (tt0) cc_final: 0.7202 (tt0) REVERT: B 370 GLN cc_start: 0.7254 (mt0) cc_final: 0.6699 (mm110) REVERT: B 380 LYS cc_start: 0.7150 (mtpt) cc_final: 0.6825 (mtpm) REVERT: B 440 ASN cc_start: 0.7117 (p0) cc_final: 0.6679 (p0) REVERT: B 441 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: B 457 LYS cc_start: 0.7861 (mtpp) cc_final: 0.7647 (ttpp) REVERT: B 463 ASN cc_start: 0.7936 (t0) cc_final: 0.7330 (t0) REVERT: B 465 GLU cc_start: 0.7806 (tp30) cc_final: 0.7562 (tp30) REVERT: B 466 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7035 (mm-30) REVERT: B 485 LYS cc_start: 0.7497 (ttpp) cc_final: 0.7219 (ttpp) REVERT: B 492 TYR cc_start: 0.8082 (t80) cc_final: 0.7395 (t80) REVERT: B 521 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7298 (tm-30) REVERT: C 10 PHE cc_start: 0.6473 (t80) cc_final: 0.6201 (t80) REVERT: C 16 MET cc_start: 0.7495 (ttp) cc_final: 0.7081 (ptp) REVERT: C 33 PHE cc_start: 0.7362 (t80) cc_final: 0.7016 (t80) REVERT: C 61 LYS cc_start: 0.7807 (ttmt) cc_final: 0.7236 (ttmm) REVERT: C 66 GLU cc_start: 0.7632 (pt0) cc_final: 0.6888 (pm20) REVERT: C 99 GLU cc_start: 0.7460 (tt0) cc_final: 0.7228 (tt0) REVERT: C 110 SER cc_start: 0.8010 (t) cc_final: 0.7466 (p) REVERT: C 120 LYS cc_start: 0.7725 (mttt) cc_final: 0.7512 (ttmm) REVERT: C 156 GLU cc_start: 0.7711 (tt0) cc_final: 0.7164 (pm20) REVERT: C 203 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7149 (mm-30) REVERT: C 232 LYS cc_start: 0.8435 (mttt) cc_final: 0.8068 (mttp) REVERT: C 234 ASP cc_start: 0.8065 (m-30) cc_final: 0.7835 (p0) REVERT: C 288 ARG cc_start: 0.7477 (mtp85) cc_final: 0.6884 (mtm180) REVERT: C 301 SER cc_start: 0.7642 (t) cc_final: 0.7372 (m) REVERT: C 312 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (ttp-170) REVERT: C 346 ASN cc_start: 0.7729 (m-40) cc_final: 0.7436 (m-40) REVERT: C 370 GLN cc_start: 0.7303 (mt0) cc_final: 0.6824 (mp10) REVERT: C 380 LYS cc_start: 0.7624 (mtpt) cc_final: 0.7064 (mtpp) REVERT: C 438 LYS cc_start: 0.7843 (mttt) cc_final: 0.7514 (mttm) REVERT: C 462 SER cc_start: 0.8410 (m) cc_final: 0.7995 (t) REVERT: C 463 ASN cc_start: 0.8053 (t0) cc_final: 0.7260 (t0) REVERT: C 465 GLU cc_start: 0.7830 (tp30) cc_final: 0.7573 (tp30) REVERT: C 466 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7204 (mm-30) REVERT: C 488 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7215 (mt-10) REVERT: C 494 ARG cc_start: 0.6842 (ttp-110) cc_final: 0.6588 (ttp-110) REVERT: C 521 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7241 (tm-30) outliers start: 36 outliers final: 15 residues processed: 399 average time/residue: 1.5354 time to fit residues: 657.0024 Evaluate side-chains 385 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 366 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 501 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 3.9990 chunk 85 optimal weight: 0.0000 chunk 2 optimal weight: 8.9990 chunk 112 optimal weight: 0.0470 chunk 62 optimal weight: 0.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.6088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS A 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS B 482 ASN C 141 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13227 Z= 0.329 Angle : 0.602 14.382 17910 Z= 0.311 Chirality : 0.046 0.264 1950 Planarity : 0.005 0.063 2307 Dihedral : 4.635 26.835 2040 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.64 % Allowed : 18.34 % Favored : 79.01 % 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: 1.44 (0.21), residues: 1563 helix: 1.57 (0.20), residues: 687 sheet: 0.87 (0.28), residues: 276 loop : 0.43 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 349 HIS 0.005 0.001 HIS B 260 PHE 0.017 0.002 PHE C 439 TYR 0.015 0.002 TYR A 118 ARG 0.005 0.000 ARG B 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 373 time to evaluate : 1.564 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7923 (mmmm) cc_final: 0.7505 (tptp) REVERT: A 15 THR cc_start: 0.7703 (p) cc_final: 0.7389 (p) REVERT: A 44 MET cc_start: 0.7509 (ttt) cc_final: 0.7108 (ttt) REVERT: A 49 MET cc_start: 0.6286 (ttt) cc_final: 0.5967 (tmm) REVERT: A 61 LYS cc_start: 0.7981 (ttmt) cc_final: 0.7576 (mtpm) REVERT: A 102 ARG cc_start: 0.7200 (mtm-85) cc_final: 0.6979 (mtm180) REVERT: A 178 ARG cc_start: 0.7544 (ttm170) cc_final: 0.7222 (mtm-85) REVERT: A 203 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 232 LYS cc_start: 0.8516 (mttt) cc_final: 0.8201 (mttm) REVERT: A 288 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7082 (mtp180) REVERT: A 289 ARG cc_start: 0.7656 (OUTLIER) cc_final: 0.6756 (ttt90) REVERT: A 302 ASP cc_start: 0.7295 (p0) cc_final: 0.7043 (p0) REVERT: A 380 LYS cc_start: 0.6434 (mtpt) cc_final: 0.6157 (mttp) REVERT: A 406 ASP cc_start: 0.7598 (t0) cc_final: 0.7109 (t0) REVERT: A 407 GLU cc_start: 0.7385 (tt0) cc_final: 0.7146 (tt0) REVERT: A 438 LYS cc_start: 0.7887 (mttt) cc_final: 0.7639 (mtpp) REVERT: A 465 GLU cc_start: 0.7738 (tp30) cc_final: 0.7448 (tp30) REVERT: A 470 ASP cc_start: 0.7817 (m-30) cc_final: 0.7429 (m-30) REVERT: A 518 GLU cc_start: 0.7370 (tp30) cc_final: 0.7144 (tp30) REVERT: A 521 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 16 MET cc_start: 0.7324 (ttp) cc_final: 0.6998 (ptm) REVERT: B 33 PHE cc_start: 0.7435 (t80) cc_final: 0.7173 (t80) REVERT: B 44 MET cc_start: 0.7375 (ttt) cc_final: 0.6859 (ttt) REVERT: B 49 MET cc_start: 0.6372 (ttt) cc_final: 0.5668 (tmm) REVERT: B 51 GLU cc_start: 0.6605 (tp30) cc_final: 0.6359 (tp30) REVERT: B 61 LYS cc_start: 0.8000 (ttmt) cc_final: 0.7641 (ttpp) REVERT: B 116 ARG cc_start: 0.7328 (mtp180) cc_final: 0.7094 (mtp85) REVERT: B 120 LYS cc_start: 0.7902 (ttmt) cc_final: 0.7654 (ttmm) REVERT: B 121 LYS cc_start: 0.7847 (ttpp) cc_final: 0.7499 (tttm) REVERT: B 156 GLU cc_start: 0.7618 (tt0) cc_final: 0.7245 (tt0) REVERT: B 203 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7371 (mm-30) REVERT: B 213 GLU cc_start: 0.7416 (pt0) cc_final: 0.7203 (pt0) REVERT: B 232 LYS cc_start: 0.8312 (mttt) cc_final: 0.8080 (mttm) REVERT: B 288 ARG cc_start: 0.7442 (mtp85) cc_final: 0.7004 (mtm-85) REVERT: B 301 SER cc_start: 0.7638 (t) cc_final: 0.7060 (p) REVERT: B 303 LYS cc_start: 0.8043 (mtmt) cc_final: 0.7522 (mtpp) REVERT: B 311 GLU cc_start: 0.6753 (mm-30) cc_final: 0.6474 (mm-30) REVERT: B 329 GLU cc_start: 0.7485 (tt0) cc_final: 0.7199 (tt0) REVERT: B 370 GLN cc_start: 0.7212 (mt0) cc_final: 0.6656 (mm110) REVERT: B 380 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6825 (mtpm) REVERT: B 440 ASN cc_start: 0.7079 (p0) cc_final: 0.6686 (p0) REVERT: B 441 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6778 (mp0) REVERT: B 457 LYS cc_start: 0.7939 (mtpp) cc_final: 0.7698 (ttpp) REVERT: B 463 ASN cc_start: 0.7888 (t0) cc_final: 0.7260 (t0) REVERT: B 465 GLU cc_start: 0.7807 (tp30) cc_final: 0.7560 (tp30) REVERT: B 466 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7013 (mm-30) REVERT: B 480 ASP cc_start: 0.7234 (m-30) cc_final: 0.6299 (p0) REVERT: B 485 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7254 (ttpp) REVERT: B 490 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7209 (tp30) REVERT: B 492 TYR cc_start: 0.8020 (t80) cc_final: 0.6998 (t80) REVERT: B 521 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7020 (tm-30) REVERT: C 10 PHE cc_start: 0.6512 (t80) cc_final: 0.6241 (t80) REVERT: C 21 LYS cc_start: 0.7260 (tppp) cc_final: 0.7036 (tppp) REVERT: C 33 PHE cc_start: 0.7417 (t80) cc_final: 0.7089 (t80) REVERT: C 44 MET cc_start: 0.7466 (ttt) cc_final: 0.7195 (ttp) REVERT: C 61 LYS cc_start: 0.7855 (ttmt) cc_final: 0.7561 (mtpm) REVERT: C 109 LYS cc_start: 0.8174 (mttp) cc_final: 0.7954 (mttm) REVERT: C 110 SER cc_start: 0.8057 (t) cc_final: 0.7513 (p) REVERT: C 120 LYS cc_start: 0.7757 (mttt) cc_final: 0.7511 (ttmm) REVERT: C 156 GLU cc_start: 0.7700 (tt0) cc_final: 0.7095 (pm20) REVERT: C 203 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7183 (mm-30) REVERT: C 232 LYS cc_start: 0.8447 (mttt) cc_final: 0.8090 (mttp) REVERT: C 234 ASP cc_start: 0.8080 (m-30) cc_final: 0.7849 (p0) REVERT: C 288 ARG cc_start: 0.7465 (mtp85) cc_final: 0.6914 (mtm-85) REVERT: C 301 SER cc_start: 0.7670 (t) cc_final: 0.7397 (m) REVERT: C 312 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7783 (ttp-170) REVERT: C 346 ASN cc_start: 0.7738 (m-40) cc_final: 0.7454 (m-40) REVERT: C 355 ASN cc_start: 0.7847 (m-40) cc_final: 0.7282 (p0) REVERT: C 363 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7075 (p) REVERT: C 370 GLN cc_start: 0.7449 (mt0) cc_final: 0.6920 (mp10) REVERT: C 380 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7067 (mtpp) REVERT: C 381 CYS cc_start: 0.7278 (m) cc_final: 0.7000 (m) REVERT: C 438 LYS cc_start: 0.7862 (mttt) cc_final: 0.7556 (mttm) REVERT: C 462 SER cc_start: 0.8427 (m) cc_final: 0.8007 (t) REVERT: C 463 ASN cc_start: 0.8100 (t0) cc_final: 0.7275 (t0) REVERT: C 465 GLU cc_start: 0.7852 (tp30) cc_final: 0.7592 (tp30) REVERT: C 466 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7167 (mm-30) REVERT: C 494 ARG cc_start: 0.6872 (ttp-110) cc_final: 0.6610 (ttp-110) REVERT: C 516 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6342 (mm) REVERT: C 521 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7214 (tm-30) outliers start: 37 outliers final: 20 residues processed: 390 average time/residue: 1.5393 time to fit residues: 643.2491 Evaluate side-chains 390 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 364 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 468 MET Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13227 Z= 0.208 Angle : 0.565 10.933 17910 Z= 0.288 Chirality : 0.043 0.253 1950 Planarity : 0.005 0.060 2307 Dihedral : 4.486 25.830 2040 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.64 % Allowed : 18.49 % Favored : 78.87 % 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: 1.62 (0.21), residues: 1563 helix: 1.77 (0.20), residues: 690 sheet: 0.91 (0.28), residues: 276 loop : 0.48 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 349 HIS 0.004 0.001 HIS B 297 PHE 0.017 0.001 PHE B 431 TYR 0.014 0.001 TYR B 118 ARG 0.004 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 370 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.7692 (p) cc_final: 0.7393 (p) REVERT: A 44 MET cc_start: 0.7395 (ttt) cc_final: 0.7000 (ttt) REVERT: A 49 MET cc_start: 0.6289 (ttt) cc_final: 0.5955 (tmm) REVERT: A 61 LYS cc_start: 0.7917 (ttmt) cc_final: 0.7626 (ttmm) REVERT: A 102 ARG cc_start: 0.7151 (mtm-85) cc_final: 0.6933 (mtm180) REVERT: A 232 LYS cc_start: 0.8520 (mttt) cc_final: 0.8191 (mttm) REVERT: A 288 ARG cc_start: 0.7474 (mtp85) cc_final: 0.6938 (mtm180) REVERT: A 289 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6729 (ttt90) REVERT: A 302 ASP cc_start: 0.7294 (p0) cc_final: 0.7031 (p0) REVERT: A 380 LYS cc_start: 0.6412 (mtpt) cc_final: 0.6158 (mttp) REVERT: A 406 ASP cc_start: 0.7576 (t0) cc_final: 0.7071 (t0) REVERT: A 438 LYS cc_start: 0.7897 (mttt) cc_final: 0.7685 (mtpp) REVERT: A 440 ASN cc_start: 0.7113 (p0) cc_final: 0.6718 (t0) REVERT: A 462 SER cc_start: 0.8382 (m) cc_final: 0.7832 (p) REVERT: A 465 GLU cc_start: 0.7787 (tp30) cc_final: 0.7471 (tp30) REVERT: A 470 ASP cc_start: 0.7772 (m-30) cc_final: 0.7255 (m-30) REVERT: A 518 GLU cc_start: 0.7366 (tp30) cc_final: 0.7103 (tp30) REVERT: A 521 GLU cc_start: 0.7567 (tm-30) cc_final: 0.6993 (tm-30) REVERT: B 16 MET cc_start: 0.7253 (ttp) cc_final: 0.6900 (ptm) REVERT: B 33 PHE cc_start: 0.7457 (t80) cc_final: 0.7203 (t80) REVERT: B 44 MET cc_start: 0.7359 (ttt) cc_final: 0.6832 (ttt) REVERT: B 51 GLU cc_start: 0.6604 (tp30) cc_final: 0.6383 (tp30) REVERT: B 61 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7644 (ttpp) REVERT: B 120 LYS cc_start: 0.7972 (ttmt) cc_final: 0.7728 (ttmm) REVERT: B 121 LYS cc_start: 0.7854 (ttpp) cc_final: 0.7510 (tttm) REVERT: B 156 GLU cc_start: 0.7614 (tt0) cc_final: 0.7238 (tt0) REVERT: B 178 ARG cc_start: 0.7552 (ttm170) cc_final: 0.7237 (mtm-85) REVERT: B 203 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7383 (mm-30) REVERT: B 213 GLU cc_start: 0.7279 (pt0) cc_final: 0.6941 (pt0) REVERT: B 232 LYS cc_start: 0.8327 (mttt) cc_final: 0.8064 (mttt) REVERT: B 288 ARG cc_start: 0.7434 (mtp85) cc_final: 0.6922 (mtm-85) REVERT: B 301 SER cc_start: 0.7696 (t) cc_final: 0.7107 (p) REVERT: B 303 LYS cc_start: 0.8030 (mtmt) cc_final: 0.7520 (mtpp) REVERT: B 311 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6450 (mm-30) REVERT: B 329 GLU cc_start: 0.7458 (tt0) cc_final: 0.7165 (tt0) REVERT: B 370 GLN cc_start: 0.7212 (mt0) cc_final: 0.6640 (mm110) REVERT: B 380 LYS cc_start: 0.7158 (mtpt) cc_final: 0.6813 (mtpm) REVERT: B 438 LYS cc_start: 0.7963 (mttt) cc_final: 0.7681 (mtpp) REVERT: B 440 ASN cc_start: 0.7004 (p0) cc_final: 0.6326 (p0) REVERT: B 441 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: B 457 LYS cc_start: 0.7949 (mtpp) cc_final: 0.7685 (ttpp) REVERT: B 463 ASN cc_start: 0.7896 (t0) cc_final: 0.7185 (t0) REVERT: B 465 GLU cc_start: 0.7804 (tp30) cc_final: 0.7563 (tp30) REVERT: B 466 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7015 (mm-30) REVERT: B 485 LYS cc_start: 0.7518 (ttpp) cc_final: 0.7246 (ttpp) REVERT: B 492 TYR cc_start: 0.8022 (t80) cc_final: 0.7266 (t80) REVERT: B 494 ARG cc_start: 0.6984 (ttm-80) cc_final: 0.6774 (ttm-80) REVERT: B 521 GLU cc_start: 0.7630 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 10 PHE cc_start: 0.6561 (t80) cc_final: 0.6263 (t80) REVERT: C 16 MET cc_start: 0.7550 (ttp) cc_final: 0.7019 (ptp) REVERT: C 33 PHE cc_start: 0.7436 (t80) cc_final: 0.7069 (t80) REVERT: C 44 MET cc_start: 0.7443 (OUTLIER) cc_final: 0.7186 (ttp) REVERT: C 61 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7360 (mtpm) REVERT: C 110 SER cc_start: 0.8080 (t) cc_final: 0.7558 (p) REVERT: C 120 LYS cc_start: 0.7764 (mttt) cc_final: 0.7495 (ttmm) REVERT: C 156 GLU cc_start: 0.7682 (tt0) cc_final: 0.7291 (tt0) REVERT: C 203 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7200 (mm-30) REVERT: C 232 LYS cc_start: 0.8417 (mttt) cc_final: 0.8039 (mttp) REVERT: C 234 ASP cc_start: 0.8065 (m-30) cc_final: 0.7836 (p0) REVERT: C 288 ARG cc_start: 0.7443 (mtp85) cc_final: 0.6862 (mtm-85) REVERT: C 301 SER cc_start: 0.7633 (t) cc_final: 0.7387 (m) REVERT: C 312 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7809 (ttp-170) REVERT: C 346 ASN cc_start: 0.7744 (m-40) cc_final: 0.7451 (m-40) REVERT: C 355 ASN cc_start: 0.7809 (m-40) cc_final: 0.7264 (p0) REVERT: C 370 GLN cc_start: 0.7456 (mt0) cc_final: 0.6893 (mp10) REVERT: C 380 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7066 (mtpp) REVERT: C 381 CYS cc_start: 0.7272 (m) cc_final: 0.6854 (p) REVERT: C 438 LYS cc_start: 0.7861 (mttt) cc_final: 0.7462 (mttm) REVERT: C 462 SER cc_start: 0.8427 (m) cc_final: 0.8018 (p) REVERT: C 463 ASN cc_start: 0.8088 (t0) cc_final: 0.7254 (t0) REVERT: C 465 GLU cc_start: 0.7857 (tp30) cc_final: 0.7591 (tp30) REVERT: C 466 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7159 (mm-30) REVERT: C 494 ARG cc_start: 0.6866 (ttp-110) cc_final: 0.6588 (ttp-110) REVERT: C 495 ASN cc_start: 0.6991 (t0) cc_final: 0.6588 (t0) REVERT: C 516 LEU cc_start: 0.6737 (OUTLIER) cc_final: 0.6389 (mm) REVERT: C 521 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7223 (tm-30) outliers start: 37 outliers final: 17 residues processed: 388 average time/residue: 1.5067 time to fit residues: 627.2272 Evaluate side-chains 386 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 364 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 270 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 85 optimal weight: 0.0980 chunk 110 optimal weight: 0.0170 chunk 127 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 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 297 HIS ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13227 Z= 0.174 Angle : 0.549 9.696 17910 Z= 0.278 Chirality : 0.042 0.248 1950 Planarity : 0.004 0.059 2307 Dihedral : 4.313 25.516 2040 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.43 % Allowed : 19.27 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.21), residues: 1563 helix: 1.93 (0.20), residues: 690 sheet: 1.04 (0.29), residues: 276 loop : 0.52 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 219 HIS 0.003 0.000 HIS A 260 PHE 0.018 0.001 PHE A 33 TYR 0.014 0.001 TYR A 118 ARG 0.003 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 367 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7909 (mmmm) cc_final: 0.7411 (tptp) REVERT: A 15 THR cc_start: 0.7640 (p) cc_final: 0.7346 (p) REVERT: A 44 MET cc_start: 0.7338 (ttt) cc_final: 0.6932 (ttt) REVERT: A 49 MET cc_start: 0.6273 (ttt) cc_final: 0.5946 (tmm) REVERT: A 61 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7627 (mtpm) REVERT: A 102 ARG cc_start: 0.7094 (mtm-85) cc_final: 0.6888 (mtm180) REVERT: A 178 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7098 (mtm-85) REVERT: A 232 LYS cc_start: 0.8462 (mttt) cc_final: 0.8152 (mttm) REVERT: A 288 ARG cc_start: 0.7482 (mtp85) cc_final: 0.6956 (mtm-85) REVERT: A 289 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.6789 (ttt90) REVERT: A 302 ASP cc_start: 0.7274 (p0) cc_final: 0.7008 (p0) REVERT: A 380 LYS cc_start: 0.6366 (mtpt) cc_final: 0.6150 (mmmm) REVERT: A 407 GLU cc_start: 0.7357 (tt0) cc_final: 0.7143 (tt0) REVERT: A 440 ASN cc_start: 0.7035 (p0) cc_final: 0.6733 (t0) REVERT: A 462 SER cc_start: 0.8373 (m) cc_final: 0.7818 (p) REVERT: A 465 GLU cc_start: 0.7778 (tp30) cc_final: 0.7474 (tp30) REVERT: A 470 ASP cc_start: 0.7800 (m-30) cc_final: 0.7325 (m-30) REVERT: A 518 GLU cc_start: 0.7364 (tp30) cc_final: 0.7103 (tp30) REVERT: A 521 GLU cc_start: 0.7586 (tm-30) cc_final: 0.7003 (tm-30) REVERT: B 16 MET cc_start: 0.7206 (ttp) cc_final: 0.6788 (ptm) REVERT: B 33 PHE cc_start: 0.7467 (t80) cc_final: 0.7219 (t80) REVERT: B 44 MET cc_start: 0.7368 (ttt) cc_final: 0.6907 (ttt) REVERT: B 51 GLU cc_start: 0.6609 (tp30) cc_final: 0.6394 (tp30) REVERT: B 61 LYS cc_start: 0.7960 (ttmt) cc_final: 0.7642 (ttpp) REVERT: B 80 CYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8351 (m) REVERT: B 120 LYS cc_start: 0.7977 (ttmt) cc_final: 0.7726 (ttmm) REVERT: B 121 LYS cc_start: 0.7811 (ttpp) cc_final: 0.7459 (tttm) REVERT: B 156 GLU cc_start: 0.7610 (tt0) cc_final: 0.7226 (tt0) REVERT: B 178 ARG cc_start: 0.7558 (ttm170) cc_final: 0.7274 (mtm-85) REVERT: B 232 LYS cc_start: 0.8322 (mttt) cc_final: 0.8047 (mttm) REVERT: B 288 ARG cc_start: 0.7376 (mtp85) cc_final: 0.6903 (mtm-85) REVERT: B 301 SER cc_start: 0.7618 (t) cc_final: 0.7034 (p) REVERT: B 303 LYS cc_start: 0.7996 (mtmt) cc_final: 0.7471 (mtpp) REVERT: B 311 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6433 (mm-30) REVERT: B 326 TYR cc_start: 0.7154 (m-80) cc_final: 0.6532 (m-10) REVERT: B 329 GLU cc_start: 0.7444 (tt0) cc_final: 0.7183 (tt0) REVERT: B 370 GLN cc_start: 0.7204 (mt0) cc_final: 0.6703 (mm110) REVERT: B 380 LYS cc_start: 0.7139 (mtpt) cc_final: 0.6795 (mtpm) REVERT: B 438 LYS cc_start: 0.7937 (mttt) cc_final: 0.7692 (mmmt) REVERT: B 440 ASN cc_start: 0.6924 (p0) cc_final: 0.6363 (p0) REVERT: B 441 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: B 457 LYS cc_start: 0.7942 (mtpp) cc_final: 0.7676 (ttpp) REVERT: B 463 ASN cc_start: 0.7900 (t0) cc_final: 0.7165 (t0) REVERT: B 465 GLU cc_start: 0.7783 (tp30) cc_final: 0.7535 (tp30) REVERT: B 466 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7059 (mm-30) REVERT: B 485 LYS cc_start: 0.7512 (ttpp) cc_final: 0.7226 (ttpp) REVERT: B 492 TYR cc_start: 0.7952 (t80) cc_final: 0.7005 (t80) REVERT: B 494 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6783 (ttm-80) REVERT: B 521 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7320 (tm-30) REVERT: C 10 PHE cc_start: 0.6637 (t80) cc_final: 0.6323 (t80) REVERT: C 33 PHE cc_start: 0.7388 (t80) cc_final: 0.7017 (t80) REVERT: C 44 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7209 (ttp) REVERT: C 51 GLU cc_start: 0.6928 (tp30) cc_final: 0.6682 (tm-30) REVERT: C 61 LYS cc_start: 0.7781 (ttmt) cc_final: 0.7439 (ttmm) REVERT: C 80 CYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8412 (m) REVERT: C 110 SER cc_start: 0.8089 (t) cc_final: 0.7619 (p) REVERT: C 120 LYS cc_start: 0.7762 (mttt) cc_final: 0.7496 (ttmm) REVERT: C 156 GLU cc_start: 0.7610 (tt0) cc_final: 0.7256 (tt0) REVERT: C 203 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7233 (mm-30) REVERT: C 232 LYS cc_start: 0.8412 (mttt) cc_final: 0.8052 (mttp) REVERT: C 234 ASP cc_start: 0.8055 (m-30) cc_final: 0.7825 (p0) REVERT: C 288 ARG cc_start: 0.7382 (mtp85) cc_final: 0.6746 (mtm180) REVERT: C 301 SER cc_start: 0.7618 (t) cc_final: 0.7377 (m) REVERT: C 312 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7590 (ttp-170) REVERT: C 346 ASN cc_start: 0.7748 (m-40) cc_final: 0.7453 (m-40) REVERT: C 355 ASN cc_start: 0.7780 (m-40) cc_final: 0.7387 (p0) REVERT: C 370 GLN cc_start: 0.7420 (mt0) cc_final: 0.6880 (mp10) REVERT: C 380 LYS cc_start: 0.7682 (mtpt) cc_final: 0.7078 (mtpp) REVERT: C 381 CYS cc_start: 0.7228 (m) cc_final: 0.6850 (p) REVERT: C 462 SER cc_start: 0.8425 (m) cc_final: 0.7996 (t) REVERT: C 463 ASN cc_start: 0.8100 (t0) cc_final: 0.7228 (t0) REVERT: C 465 GLU cc_start: 0.7912 (tp30) cc_final: 0.7634 (tp30) REVERT: C 466 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7173 (mm-30) REVERT: C 494 ARG cc_start: 0.6853 (ttp-110) cc_final: 0.6589 (ttp-110) REVERT: C 495 ASN cc_start: 0.7062 (t0) cc_final: 0.6642 (t0) REVERT: C 516 LEU cc_start: 0.6734 (OUTLIER) cc_final: 0.6396 (mm) REVERT: C 521 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7142 (tm-30) outliers start: 34 outliers final: 18 residues processed: 383 average time/residue: 1.5498 time to fit residues: 636.5238 Evaluate side-chains 388 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 363 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 95 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 14 optimal weight: 0.5980 chunk 118 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS B 152 ASN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 243 HIS ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13227 Z= 0.178 Angle : 0.573 13.935 17910 Z= 0.286 Chirality : 0.043 0.246 1950 Planarity : 0.004 0.060 2307 Dihedral : 4.222 25.463 2040 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.36 % Allowed : 19.34 % Favored : 78.30 % 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: 1.86 (0.21), residues: 1563 helix: 1.99 (0.20), residues: 690 sheet: 1.08 (0.29), residues: 276 loop : 0.53 (0.26), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 219 HIS 0.005 0.001 HIS B 297 PHE 0.024 0.001 PHE B 10 TYR 0.013 0.001 TYR B 118 ARG 0.004 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 361 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 THR cc_start: 0.7650 (p) cc_final: 0.7342 (p) REVERT: A 44 MET cc_start: 0.7322 (ttt) cc_final: 0.6919 (ttt) REVERT: A 49 MET cc_start: 0.6297 (ttt) cc_final: 0.5811 (tmm) REVERT: A 111 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7617 (mt-10) REVERT: A 178 ARG cc_start: 0.7470 (ttm170) cc_final: 0.7107 (mtm-85) REVERT: A 232 LYS cc_start: 0.8456 (mttt) cc_final: 0.8150 (mttm) REVERT: A 288 ARG cc_start: 0.7480 (mtp85) cc_final: 0.7030 (mtm-85) REVERT: A 289 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6798 (ttt90) REVERT: A 302 ASP cc_start: 0.7267 (p0) cc_final: 0.6999 (p0) REVERT: A 407 GLU cc_start: 0.7388 (tt0) cc_final: 0.7149 (tt0) REVERT: A 440 ASN cc_start: 0.6990 (p0) cc_final: 0.6745 (t0) REVERT: A 462 SER cc_start: 0.8494 (m) cc_final: 0.7933 (p) REVERT: A 465 GLU cc_start: 0.7774 (tp30) cc_final: 0.7475 (tp30) REVERT: A 470 ASP cc_start: 0.7743 (m-30) cc_final: 0.7301 (m-30) REVERT: A 518 GLU cc_start: 0.7323 (tp30) cc_final: 0.7018 (tp30) REVERT: A 521 GLU cc_start: 0.7559 (tm-30) cc_final: 0.7018 (tm-30) REVERT: B 33 PHE cc_start: 0.7473 (t80) cc_final: 0.7228 (t80) REVERT: B 44 MET cc_start: 0.7357 (OUTLIER) cc_final: 0.6900 (ttt) REVERT: B 61 LYS cc_start: 0.7934 (ttmt) cc_final: 0.7618 (ttpp) REVERT: B 80 CYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8364 (m) REVERT: B 109 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7968 (mttt) REVERT: B 110 SER cc_start: 0.8420 (t) cc_final: 0.7813 (t) REVERT: B 111 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7475 (mm-30) REVERT: B 120 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7721 (ttmm) REVERT: B 121 LYS cc_start: 0.7830 (ttpp) cc_final: 0.7461 (tttp) REVERT: B 156 GLU cc_start: 0.7610 (tt0) cc_final: 0.7408 (mm-30) REVERT: B 203 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7403 (mm-30) REVERT: B 232 LYS cc_start: 0.8337 (mttt) cc_final: 0.8064 (mttm) REVERT: B 235 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7512 (pt0) REVERT: B 288 ARG cc_start: 0.7369 (mtp85) cc_final: 0.6886 (mtm-85) REVERT: B 301 SER cc_start: 0.7619 (t) cc_final: 0.7053 (p) REVERT: B 303 LYS cc_start: 0.7973 (mtmt) cc_final: 0.7472 (mtpp) REVERT: B 311 GLU cc_start: 0.6715 (mm-30) cc_final: 0.6439 (mm-30) REVERT: B 326 TYR cc_start: 0.7152 (m-80) cc_final: 0.6613 (m-10) REVERT: B 329 GLU cc_start: 0.7439 (tt0) cc_final: 0.7184 (tt0) REVERT: B 370 GLN cc_start: 0.7192 (mt0) cc_final: 0.6702 (mm110) REVERT: B 457 LYS cc_start: 0.7912 (mtpp) cc_final: 0.7643 (ttpp) REVERT: B 463 ASN cc_start: 0.7897 (t0) cc_final: 0.7133 (t0) REVERT: B 465 GLU cc_start: 0.7791 (tp30) cc_final: 0.7527 (tp30) REVERT: B 466 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7000 (mm-30) REVERT: B 485 LYS cc_start: 0.7516 (ttpp) cc_final: 0.7229 (ttpp) REVERT: B 492 TYR cc_start: 0.7761 (t80) cc_final: 0.6874 (t80) REVERT: B 494 ARG cc_start: 0.6985 (ttm-80) cc_final: 0.6782 (ttm-80) REVERT: B 521 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7385 (tm-30) REVERT: C 10 PHE cc_start: 0.6629 (t80) cc_final: 0.6314 (t80) REVERT: C 16 MET cc_start: 0.7521 (ttp) cc_final: 0.7019 (ptp) REVERT: C 33 PHE cc_start: 0.7409 (t80) cc_final: 0.7047 (t80) REVERT: C 44 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7198 (ttp) REVERT: C 51 GLU cc_start: 0.6928 (tp30) cc_final: 0.6629 (tm-30) REVERT: C 61 LYS cc_start: 0.7727 (ttmt) cc_final: 0.7443 (ttmm) REVERT: C 80 CYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8420 (m) REVERT: C 110 SER cc_start: 0.8010 (t) cc_final: 0.7553 (p) REVERT: C 120 LYS cc_start: 0.7756 (mttt) cc_final: 0.7494 (ttmm) REVERT: C 156 GLU cc_start: 0.7498 (tt0) cc_final: 0.7133 (tt0) REVERT: C 203 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7330 (mm-30) REVERT: C 232 LYS cc_start: 0.8387 (mttt) cc_final: 0.8031 (mttp) REVERT: C 234 ASP cc_start: 0.8077 (m-30) cc_final: 0.7867 (p0) REVERT: C 236 ILE cc_start: 0.8417 (mm) cc_final: 0.8216 (mp) REVERT: C 288 ARG cc_start: 0.7400 (mtp85) cc_final: 0.6782 (mtm-85) REVERT: C 301 SER cc_start: 0.7618 (t) cc_final: 0.7377 (m) REVERT: C 312 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7851 (ttp80) REVERT: C 346 ASN cc_start: 0.7747 (m-40) cc_final: 0.7454 (m-40) REVERT: C 355 ASN cc_start: 0.7762 (m-40) cc_final: 0.7446 (p0) REVERT: C 370 GLN cc_start: 0.7407 (mt0) cc_final: 0.6884 (mp10) REVERT: C 380 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7072 (mtpp) REVERT: C 381 CYS cc_start: 0.7211 (m) cc_final: 0.6856 (p) REVERT: C 462 SER cc_start: 0.8419 (m) cc_final: 0.7986 (t) REVERT: C 463 ASN cc_start: 0.8062 (t0) cc_final: 0.7216 (t0) REVERT: C 465 GLU cc_start: 0.7913 (tp30) cc_final: 0.7633 (tp30) REVERT: C 466 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7165 (mm-30) REVERT: C 494 ARG cc_start: 0.6843 (ttp-110) cc_final: 0.6588 (ttp-110) REVERT: C 495 ASN cc_start: 0.7067 (t0) cc_final: 0.6644 (t0) REVERT: C 516 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6486 (mm) REVERT: C 521 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7105 (tm-30) outliers start: 33 outliers final: 22 residues processed: 376 average time/residue: 1.4699 time to fit residues: 594.2678 Evaluate side-chains 391 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 361 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 139 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13227 Z= 0.222 Angle : 0.585 12.775 17910 Z= 0.294 Chirality : 0.043 0.250 1950 Planarity : 0.005 0.059 2307 Dihedral : 4.225 25.830 2040 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 19.70 % Favored : 77.87 % 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: 1.85 (0.21), residues: 1563 helix: 2.01 (0.20), residues: 684 sheet: 1.13 (0.29), residues: 276 loop : 0.48 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 219 HIS 0.006 0.001 HIS B 297 PHE 0.019 0.001 PHE A 33 TYR 0.014 0.001 TYR B 118 ARG 0.005 0.000 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 365 time to evaluate : 1.335 Fit side-chains REVERT: A 9 LYS cc_start: 0.7907 (mmmm) cc_final: 0.7418 (tptp) REVERT: A 15 THR cc_start: 0.7714 (p) cc_final: 0.7402 (p) REVERT: A 44 MET cc_start: 0.7361 (ttt) cc_final: 0.6958 (ttt) REVERT: A 49 MET cc_start: 0.6300 (ttt) cc_final: 0.5809 (tmm) REVERT: A 111 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7618 (mt-10) REVERT: A 178 ARG cc_start: 0.7491 (ttm170) cc_final: 0.7232 (mtm-85) REVERT: A 213 GLU cc_start: 0.7274 (pt0) cc_final: 0.6993 (pt0) REVERT: A 232 LYS cc_start: 0.8459 (mttt) cc_final: 0.8159 (mttm) REVERT: A 288 ARG cc_start: 0.7483 (mtp85) cc_final: 0.7089 (mtp180) REVERT: A 289 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6787 (ttt90) REVERT: A 302 ASP cc_start: 0.7266 (p0) cc_final: 0.7004 (p0) REVERT: A 352 ASP cc_start: 0.7242 (t0) cc_final: 0.6687 (t0) REVERT: A 354 ASP cc_start: 0.7468 (m-30) cc_final: 0.6970 (m-30) REVERT: A 407 GLU cc_start: 0.7382 (tt0) cc_final: 0.7175 (tt0) REVERT: A 440 ASN cc_start: 0.7000 (p0) cc_final: 0.6738 (t0) REVERT: A 462 SER cc_start: 0.8351 (m) cc_final: 0.7797 (p) REVERT: A 465 GLU cc_start: 0.7783 (tp30) cc_final: 0.7479 (tp30) REVERT: A 470 ASP cc_start: 0.7784 (m-30) cc_final: 0.7278 (m-30) REVERT: A 490 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: A 518 GLU cc_start: 0.7263 (tp30) cc_final: 0.6840 (tp30) REVERT: A 521 GLU cc_start: 0.7534 (tm-30) cc_final: 0.6990 (tm-30) REVERT: B 16 MET cc_start: 0.7422 (ttp) cc_final: 0.6899 (ptp) REVERT: B 21 LYS cc_start: 0.7175 (tppp) cc_final: 0.6962 (tppp) REVERT: B 33 PHE cc_start: 0.7492 (t80) cc_final: 0.7250 (t80) REVERT: B 44 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.6945 (ttt) REVERT: B 51 GLU cc_start: 0.6716 (tp30) cc_final: 0.6512 (tp30) REVERT: B 61 LYS cc_start: 0.7928 (ttmt) cc_final: 0.7637 (ttpp) REVERT: B 80 CYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8311 (m) REVERT: B 109 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7962 (mttt) REVERT: B 110 SER cc_start: 0.8430 (t) cc_final: 0.8080 (t) REVERT: B 120 LYS cc_start: 0.7901 (ttmt) cc_final: 0.7660 (ttmm) REVERT: B 121 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7498 (tttp) REVERT: B 156 GLU cc_start: 0.7609 (tt0) cc_final: 0.7222 (tt0) REVERT: B 232 LYS cc_start: 0.8336 (mttt) cc_final: 0.8068 (mttm) REVERT: B 253 GLU cc_start: 0.8057 (tt0) cc_final: 0.7827 (tt0) REVERT: B 288 ARG cc_start: 0.7446 (mtp85) cc_final: 0.6935 (mtm-85) REVERT: B 301 SER cc_start: 0.7644 (t) cc_final: 0.7067 (p) REVERT: B 303 LYS cc_start: 0.7985 (mtmt) cc_final: 0.7485 (mtpp) REVERT: B 311 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6480 (mm-30) REVERT: B 326 TYR cc_start: 0.7185 (m-80) cc_final: 0.6622 (m-10) REVERT: B 329 GLU cc_start: 0.7441 (tt0) cc_final: 0.7184 (tt0) REVERT: B 370 GLN cc_start: 0.7197 (mt0) cc_final: 0.6708 (mm110) REVERT: B 441 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: B 457 LYS cc_start: 0.7946 (mtpp) cc_final: 0.7674 (ttpp) REVERT: B 463 ASN cc_start: 0.7897 (t0) cc_final: 0.7135 (t0) REVERT: B 465 GLU cc_start: 0.7796 (tp30) cc_final: 0.7442 (tp30) REVERT: B 466 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7144 (mm-30) REVERT: B 480 ASP cc_start: 0.7284 (m-30) cc_final: 0.6265 (p0) REVERT: B 485 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7276 (ttpp) REVERT: B 492 TYR cc_start: 0.7719 (t80) cc_final: 0.7217 (t80) REVERT: B 494 ARG cc_start: 0.6983 (ttm-80) cc_final: 0.6766 (ttm-80) REVERT: B 521 GLU cc_start: 0.7644 (tm-30) cc_final: 0.6969 (tm-30) REVERT: C 10 PHE cc_start: 0.6511 (t80) cc_final: 0.6220 (t80) REVERT: C 16 MET cc_start: 0.7521 (ttp) cc_final: 0.6987 (ptp) REVERT: C 33 PHE cc_start: 0.7430 (t80) cc_final: 0.7048 (t80) REVERT: C 44 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7233 (ttp) REVERT: C 51 GLU cc_start: 0.6984 (tp30) cc_final: 0.6707 (tm-30) REVERT: C 61 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7441 (ttmm) REVERT: C 80 CYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8423 (m) REVERT: C 110 SER cc_start: 0.8028 (t) cc_final: 0.7570 (p) REVERT: C 120 LYS cc_start: 0.7759 (mttt) cc_final: 0.7493 (ttmm) REVERT: C 156 GLU cc_start: 0.7488 (tt0) cc_final: 0.7132 (tt0) REVERT: C 203 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7345 (mm-30) REVERT: C 232 LYS cc_start: 0.8438 (mttt) cc_final: 0.8084 (mttp) REVERT: C 234 ASP cc_start: 0.8052 (m-30) cc_final: 0.7819 (p0) REVERT: C 288 ARG cc_start: 0.7416 (mtp85) cc_final: 0.6862 (mtm-85) REVERT: C 301 SER cc_start: 0.7640 (t) cc_final: 0.7398 (m) REVERT: C 312 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7813 (ttp-170) REVERT: C 346 ASN cc_start: 0.7754 (m-40) cc_final: 0.7464 (m-40) REVERT: C 355 ASN cc_start: 0.7747 (m-40) cc_final: 0.7467 (p0) REVERT: C 370 GLN cc_start: 0.7411 (mt0) cc_final: 0.6894 (mp10) REVERT: C 380 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7108 (mtpm) REVERT: C 381 CYS cc_start: 0.7229 (m) cc_final: 0.6879 (p) REVERT: C 462 SER cc_start: 0.8426 (m) cc_final: 0.8001 (t) REVERT: C 463 ASN cc_start: 0.8071 (t0) cc_final: 0.7193 (t0) REVERT: C 465 GLU cc_start: 0.7919 (tp30) cc_final: 0.7629 (tp30) REVERT: C 466 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7157 (mm-30) REVERT: C 494 ARG cc_start: 0.6857 (ttp-110) cc_final: 0.6598 (ttp-110) REVERT: C 495 ASN cc_start: 0.7064 (t0) cc_final: 0.6650 (t0) REVERT: C 516 LEU cc_start: 0.6910 (OUTLIER) cc_final: 0.6583 (mm) REVERT: C 521 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7096 (tm-30) outliers start: 34 outliers final: 22 residues processed: 378 average time/residue: 1.5143 time to fit residues: 614.0241 Evaluate side-chains 393 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 361 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 0.4980 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 143 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 13227 Z= 0.209 Angle : 0.592 12.170 17910 Z= 0.296 Chirality : 0.043 0.249 1950 Planarity : 0.005 0.058 2307 Dihedral : 4.203 25.522 2040 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.28 % Allowed : 20.34 % Favored : 77.37 % 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: 1.86 (0.21), residues: 1563 helix: 2.00 (0.20), residues: 687 sheet: 1.16 (0.29), residues: 276 loop : 0.48 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 219 HIS 0.006 0.001 HIS B 297 PHE 0.026 0.001 PHE B 10 TYR 0.013 0.001 TYR A 118 ARG 0.004 0.000 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3126 Ramachandran restraints generated. 1563 Oldfield, 0 Emsley, 1563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 365 time to evaluate : 1.519 Fit side-chains revert: symmetry clash REVERT: A 9 LYS cc_start: 0.7836 (mmmm) cc_final: 0.7344 (tptp) REVERT: A 15 THR cc_start: 0.7740 (p) cc_final: 0.7432 (p) REVERT: A 44 MET cc_start: 0.7353 (ttt) cc_final: 0.6955 (ttt) REVERT: A 49 MET cc_start: 0.6290 (ttt) cc_final: 0.5799 (tmm) REVERT: A 111 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7616 (mt-10) REVERT: A 178 ARG cc_start: 0.7486 (ttm170) cc_final: 0.7230 (mtm-85) REVERT: A 213 GLU cc_start: 0.7272 (pt0) cc_final: 0.6994 (pt0) REVERT: A 232 LYS cc_start: 0.8459 (mttt) cc_final: 0.8166 (mttm) REVERT: A 288 ARG cc_start: 0.7485 (mtp85) cc_final: 0.7092 (mtp180) REVERT: A 289 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.6779 (ttt90) REVERT: A 302 ASP cc_start: 0.7275 (p0) cc_final: 0.7009 (p0) REVERT: A 352 ASP cc_start: 0.7254 (t0) cc_final: 0.6991 (t0) REVERT: A 407 GLU cc_start: 0.7377 (tt0) cc_final: 0.7156 (tt0) REVERT: A 440 ASN cc_start: 0.6972 (p0) cc_final: 0.6741 (t0) REVERT: A 462 SER cc_start: 0.8506 (m) cc_final: 0.7933 (p) REVERT: A 465 GLU cc_start: 0.7797 (tp30) cc_final: 0.7510 (tp30) REVERT: A 470 ASP cc_start: 0.7784 (m-30) cc_final: 0.7295 (m-30) REVERT: A 518 GLU cc_start: 0.7257 (tp30) cc_final: 0.7036 (tp30) REVERT: A 521 GLU cc_start: 0.7482 (tm-30) cc_final: 0.6967 (tm-30) REVERT: B 16 MET cc_start: 0.7376 (ttp) cc_final: 0.7143 (ptm) REVERT: B 33 PHE cc_start: 0.7493 (t80) cc_final: 0.7223 (t80) REVERT: B 44 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6874 (ttt) REVERT: B 51 GLU cc_start: 0.6737 (tp30) cc_final: 0.6527 (tp30) REVERT: B 61 LYS cc_start: 0.7911 (ttmt) cc_final: 0.7614 (ttpp) REVERT: B 80 CYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8355 (m) REVERT: B 109 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7958 (mttt) REVERT: B 110 SER cc_start: 0.8446 (t) cc_final: 0.8075 (t) REVERT: B 120 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7659 (ttmm) REVERT: B 121 LYS cc_start: 0.7815 (ttpp) cc_final: 0.7451 (tttp) REVERT: B 156 GLU cc_start: 0.7603 (tt0) cc_final: 0.7217 (tt0) REVERT: B 178 ARG cc_start: 0.7564 (ttm170) cc_final: 0.7094 (ttm170) REVERT: B 213 GLU cc_start: 0.7268 (pt0) cc_final: 0.6530 (pt0) REVERT: B 232 LYS cc_start: 0.8326 (mttt) cc_final: 0.8048 (mttm) REVERT: B 244 GLU cc_start: 0.7712 (tp30) cc_final: 0.7331 (tp30) REVERT: B 288 ARG cc_start: 0.7435 (mtp85) cc_final: 0.6930 (mtm-85) REVERT: B 301 SER cc_start: 0.7664 (t) cc_final: 0.7355 (m) REVERT: B 303 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7456 (mtpp) REVERT: B 311 GLU cc_start: 0.6787 (mm-30) cc_final: 0.6464 (mm-30) REVERT: B 326 TYR cc_start: 0.7158 (m-80) cc_final: 0.6609 (m-10) REVERT: B 329 GLU cc_start: 0.7438 (tt0) cc_final: 0.7183 (tt0) REVERT: B 370 GLN cc_start: 0.7195 (mt0) cc_final: 0.6725 (mm110) REVERT: B 457 LYS cc_start: 0.7905 (mtpp) cc_final: 0.7629 (ttpp) REVERT: B 463 ASN cc_start: 0.7913 (t0) cc_final: 0.7148 (t0) REVERT: B 465 GLU cc_start: 0.7786 (tp30) cc_final: 0.7505 (tp30) REVERT: B 466 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7156 (mm-30) REVERT: B 480 ASP cc_start: 0.7279 (m-30) cc_final: 0.6265 (p0) REVERT: B 485 LYS cc_start: 0.7495 (ttpp) cc_final: 0.7209 (ttpp) REVERT: B 492 TYR cc_start: 0.7867 (t80) cc_final: 0.7160 (t80) REVERT: B 494 ARG cc_start: 0.6986 (ttm-80) cc_final: 0.6763 (ttm-80) REVERT: B 521 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7222 (tm-30) REVERT: C 10 PHE cc_start: 0.6598 (t80) cc_final: 0.6286 (t80) REVERT: C 16 MET cc_start: 0.7555 (ttp) cc_final: 0.7036 (ptp) REVERT: C 33 PHE cc_start: 0.7386 (t80) cc_final: 0.7014 (t80) REVERT: C 44 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7260 (ttp) REVERT: C 51 GLU cc_start: 0.7001 (tp30) cc_final: 0.6720 (tm-30) REVERT: C 61 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7004 (ttmm) REVERT: C 80 CYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8428 (m) REVERT: C 110 SER cc_start: 0.8042 (t) cc_final: 0.7587 (p) REVERT: C 120 LYS cc_start: 0.7754 (mttt) cc_final: 0.7490 (ttmm) REVERT: C 156 GLU cc_start: 0.7484 (tt0) cc_final: 0.7127 (tt0) REVERT: C 203 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7353 (mm-30) REVERT: C 232 LYS cc_start: 0.8437 (mttt) cc_final: 0.8099 (mttp) REVERT: C 234 ASP cc_start: 0.8078 (m-30) cc_final: 0.7869 (p0) REVERT: C 288 ARG cc_start: 0.7388 (mtp85) cc_final: 0.6835 (mtm-85) REVERT: C 301 SER cc_start: 0.7628 (t) cc_final: 0.7388 (m) REVERT: C 312 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7811 (ttp-170) REVERT: C 346 ASN cc_start: 0.7754 (m-40) cc_final: 0.7464 (m-40) REVERT: C 370 GLN cc_start: 0.7408 (mt0) cc_final: 0.6891 (mp10) REVERT: C 380 LYS cc_start: 0.7678 (mtpt) cc_final: 0.7133 (mtpm) REVERT: C 381 CYS cc_start: 0.7207 (m) cc_final: 0.6817 (p) REVERT: C 385 ILE cc_start: 0.7529 (mm) cc_final: 0.7305 (mt) REVERT: C 462 SER cc_start: 0.8424 (m) cc_final: 0.7999 (t) REVERT: C 463 ASN cc_start: 0.8067 (t0) cc_final: 0.7204 (t0) REVERT: C 465 GLU cc_start: 0.7923 (tp30) cc_final: 0.7599 (tp30) REVERT: C 466 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7139 (mm-30) REVERT: C 488 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7013 (mt-10) REVERT: C 494 ARG cc_start: 0.6851 (ttp-110) cc_final: 0.6594 (ttp-110) REVERT: C 495 ASN cc_start: 0.7064 (t0) cc_final: 0.6643 (t0) REVERT: C 516 LEU cc_start: 0.6912 (OUTLIER) cc_final: 0.6586 (mm) REVERT: C 521 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7092 (tm-30) outliers start: 32 outliers final: 23 residues processed: 379 average time/residue: 1.5074 time to fit residues: 613.5017 Evaluate side-chains 396 residues out of total 1401 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 365 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 289 ARG Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 490 GLU Chi-restraints excluded: chain A residue 524 ILE Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 57 PHE Chi-restraints excluded: chain B residue 80 CYS Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 350 CYS Chi-restraints excluded: chain B residue 529 LEU Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 57 PHE Chi-restraints excluded: chain C residue 80 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain C residue 312 ARG Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 384 SER Chi-restraints excluded: chain C residue 480 ASP Chi-restraints excluded: chain C residue 501 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 123 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 22 optimal weight: 0.1980 chunk 108 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 HIS ** C 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 482 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.122604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109644 restraints weight = 17694.660| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.98 r_work: 0.3275 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13227 Z= 0.187 Angle : 0.601 12.905 17910 Z= 0.298 Chirality : 0.042 0.246 1950 Planarity : 0.005 0.058 2307 Dihedral : 4.196 28.827 2040 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.21 % Allowed : 20.70 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.21), residues: 1563 helix: 2.07 (0.20), residues: 687 sheet: 1.21 (0.29), residues: 276 loop : 0.48 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 219 HIS 0.006 0.001 HIS B 297 PHE 0.018 0.001 PHE A 33 TYR 0.015 0.001 TYR A 118 ARG 0.004 0.000 ARG C 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8297.58 seconds wall clock time: 147 minutes 33.43 seconds (8853.43 seconds total)