Starting phenix.real_space_refine on Tue Feb 13 20:20:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/02_2024/7x1r_32947_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/02_2024/7x1r_32947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/02_2024/7x1r_32947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/02_2024/7x1r_32947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/02_2024/7x1r_32947_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/02_2024/7x1r_32947_updated.pdb" } resolution = 3.9 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Au 2 10.57 5 P 4 5.49 5 S 38 5.16 5 C 4824 2.51 5 N 1298 2.21 5 O 1442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 14": "OD1" <-> "OD2" Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 181": "OD1" <-> "OD2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A ARG 221": "NH1" <-> "NH2" Residue "A ARG 226": "NH1" <-> "NH2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 320": "OD1" <-> "OD2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 334": "OD1" <-> "OD2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 14": "OD1" <-> "OD2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B ASP 97": "OD1" <-> "OD2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 128": "OE1" <-> "OE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B ARG 221": "NH1" <-> "NH2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B GLU 238": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B GLU 433": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7608 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3750 Classifications: {'peptide': 485} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465} Chain: "B" Number of atoms: 3750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3750 Classifications: {'peptide': 485} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 465} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' AU': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' AU': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1419 SG CYS A 189 73.629 62.408 61.033 1.00 28.54 S ATOM 5169 SG CYS B 189 41.710 39.948 61.031 1.00 28.78 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="AU AU A 502 " occ=0.30 residue: pdb="AU AU B 502 " occ=0.30 Time building chain proxies: 4.68, per 1000 atoms: 0.62 Number of scatterers: 7608 At special positions: 0 Unit cell: (116.8, 104, 76.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Au 2 78.96 S 38 16.00 P 4 15.00 O 1442 8.00 N 1298 7.00 C 4824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 64 " distance=2.04 Simple disulfide: pdb=" SG CYS B 59 " - pdb=" SG CYS B 64 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1744 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 12 sheets defined 34.2% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.679A pdb=" N TYR A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 64 through 84 removed outlier: 4.127A pdb=" N ARG A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 122 Processing helix chain 'A' and resid 173 through 176 No H-bonds generated for 'chain 'A' and resid 173 through 176' Processing helix chain 'A' and resid 180 through 185 removed outlier: 4.188A pdb=" N PHE A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 343 through 358 Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 409 through 414 removed outlier: 4.563A pdb=" N ILE A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Proline residue: A 414 - end of helix Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 445 through 458 removed outlier: 4.208A pdb=" N GLY A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 467 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'B' and resid 22 through 34 removed outlier: 3.679A pdb=" N TYR B 34 " --> pdb=" O GLU B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 62 Processing helix chain 'B' and resid 64 through 84 removed outlier: 4.127A pdb=" N ARG B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 122 Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.188A pdb=" N PHE B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N SER B 185 " --> pdb=" O ASP B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'B' and resid 200 through 211 Processing helix chain 'B' and resid 230 through 243 Processing helix chain 'B' and resid 302 through 304 No H-bonds generated for 'chain 'B' and resid 302 through 304' Processing helix chain 'B' and resid 343 through 358 Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 409 through 414 removed outlier: 4.564A pdb=" N ILE B 413 " --> pdb=" O GLU B 410 " (cutoff:3.500A) Proline residue: B 414 - end of helix Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 445 through 458 removed outlier: 4.208A pdb=" N GLY B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 475 through 480 Processing sheet with id= A, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.101A pdb=" N PHE A 157 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL A 126 " --> pdb=" O VAL A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 149 through 153 removed outlier: 3.568A pdb=" N GLY A 136 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LYS A 141 " --> pdb=" O PHE A 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE A 134 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 143 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY A 132 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 163 through 165 Processing sheet with id= D, first strand: chain 'A' and resid 286 through 289 removed outlier: 6.387A pdb=" N LYS A 246 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 279 through 284 removed outlier: 5.997A pdb=" N GLN A 272 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 372 through 374 removed outlier: 6.551A pdb=" N ILE A 426 " --> pdb=" O VAL A 436 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE A 438 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS A 424 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 440 " --> pdb=" O TYR A 422 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TYR A 422 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.102A pdb=" N PHE B 157 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL B 126 " --> pdb=" O VAL B 40 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 149 through 153 removed outlier: 3.568A pdb=" N GLY B 136 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LYS B 141 " --> pdb=" O PHE B 134 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N PHE B 134 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 143 " --> pdb=" O GLY B 132 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLY B 132 " --> pdb=" O THR B 143 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 163 through 165 Processing sheet with id= J, first strand: chain 'B' and resid 286 through 289 removed outlier: 6.387A pdb=" N LYS B 246 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 279 through 284 removed outlier: 5.997A pdb=" N GLN B 272 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 372 through 374 removed outlier: 6.551A pdb=" N ILE B 426 " --> pdb=" O VAL B 436 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N PHE B 438 " --> pdb=" O LYS B 424 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 424 " --> pdb=" O PHE B 438 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL B 440 " --> pdb=" O TYR B 422 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TYR B 422 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 792 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: 2.44 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2486 1.35 - 1.47: 1858 1.47 - 1.60: 3368 1.60 - 1.72: 0 1.72 - 1.85: 52 Bond restraints: 7764 Sorted by residual: bond pdb=" O3P FAD B 501 " pdb=" P FAD B 501 " ideal model delta sigma weight residual 1.660 1.559 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3P FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.660 1.559 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5B FAD A 501 " pdb=" PA FAD A 501 " ideal model delta sigma weight residual 1.634 1.557 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O5B FAD B 501 " pdb=" PA FAD B 501 " ideal model delta sigma weight residual 1.634 1.557 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O5' FAD A 501 " pdb=" P FAD A 501 " ideal model delta sigma weight residual 1.637 1.573 0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 7759 not shown) Histogram of bond angle deviations from ideal: 99.47 - 106.36: 190 106.36 - 113.26: 4326 113.26 - 120.16: 2710 120.16 - 127.05: 3224 127.05 - 133.95: 82 Bond angle restraints: 10532 Sorted by residual: angle pdb=" N VAL A 305 " pdb=" CA VAL A 305 " pdb=" C VAL A 305 " ideal model delta sigma weight residual 113.47 109.63 3.84 1.01e+00 9.80e-01 1.45e+01 angle pdb=" N VAL B 305 " pdb=" CA VAL B 305 " pdb=" C VAL B 305 " ideal model delta sigma weight residual 113.47 109.63 3.84 1.01e+00 9.80e-01 1.45e+01 angle pdb=" C GLY A 207 " pdb=" N PHE A 208 " pdb=" CA PHE A 208 " ideal model delta sigma weight residual 121.14 115.43 5.71 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C GLY B 207 " pdb=" N PHE B 208 " pdb=" CA PHE B 208 " ideal model delta sigma weight residual 121.14 115.45 5.69 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C ARG B 221 " pdb=" N SER B 222 " pdb=" CA SER B 222 " ideal model delta sigma weight residual 122.17 117.21 4.96 1.54e+00 4.22e-01 1.04e+01 ... (remaining 10527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4241 17.52 - 35.03: 327 35.03 - 52.55: 66 52.55 - 70.06: 16 70.06 - 87.58: 16 Dihedral angle restraints: 4666 sinusoidal: 1912 harmonic: 2754 Sorted by residual: dihedral pdb=" CA CYS A 59 " pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 64 " ideal model delta sinusoidal sigma weight residual -73.00 1.60 -74.60 1 2.00e+01 2.50e-03 1.76e+01 dihedral pdb=" CA CYS B 59 " pdb=" CB CYS B 59 " pdb=" SG CYS B 59 " pdb=" SG CYS B 64 " ideal model delta sinusoidal sigma weight residual -73.00 1.55 -74.55 1 2.00e+01 2.50e-03 1.76e+01 dihedral pdb=" CA ALA B 160 " pdb=" C ALA B 160 " pdb=" N THR B 161 " pdb=" CA THR B 161 " ideal model delta harmonic sigma weight residual 180.00 -161.97 -18.03 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 4663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 653 0.034 - 0.068: 317 0.068 - 0.102: 141 0.102 - 0.136: 54 0.136 - 0.169: 9 Chirality restraints: 1174 Sorted by residual: chirality pdb=" CA PHE B 208 " pdb=" N PHE B 208 " pdb=" C PHE B 208 " pdb=" CB PHE B 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA PHE A 208 " pdb=" N PHE A 208 " pdb=" C PHE A 208 " pdb=" CB PHE A 208 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" C2B FAD B 501 " pdb=" C1B FAD B 501 " pdb=" C3B FAD B 501 " pdb=" O2B FAD B 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.70 0.16 2.00e-01 2.50e+01 6.67e-01 ... (remaining 1171 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 170 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO B 171 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 171 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 171 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 170 " 0.021 5.00e-02 4.00e+02 3.22e-02 1.66e+00 pdb=" N PRO A 171 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 171 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 171 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 208 " 0.011 2.00e-02 2.50e+03 9.59e-03 1.61e+00 pdb=" CG PHE B 208 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE B 208 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 208 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 208 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 208 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 208 " 0.002 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 973 2.74 - 3.28: 7402 3.28 - 3.82: 12485 3.82 - 4.36: 14959 4.36 - 4.90: 25619 Nonbonded interactions: 61438 Sorted by model distance: nonbonded pdb=" SG CYS B 189 " pdb="AU AU B 502 " model vdw 2.205 2.980 nonbonded pdb=" SG CYS A 189 " pdb="AU AU A 502 " model vdw 2.205 2.980 nonbonded pdb=" O LEU A 55 " pdb=" ND2 ASN A 113 " model vdw 2.207 2.520 nonbonded pdb=" O LEU B 55 " pdb=" ND2 ASN B 113 " model vdw 2.207 2.520 nonbonded pdb=" OG1 THR B 324 " pdb=" O ILE B 329 " model vdw 2.229 2.440 ... (remaining 61433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.040 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: 0.000 Extract box with map and model: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.020 Find NCS groups from input model: 0.410 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.007 0.101 7764 Z= 0.476 Angle : 0.755 8.330 10532 Z= 0.413 Chirality : 0.049 0.169 1174 Planarity : 0.004 0.032 1336 Dihedral : 14.250 87.578 2916 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.25 % Allowed : 7.02 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.91 (0.24), residues: 966 helix: 0.38 (0.27), residues: 290 sheet: -0.35 (0.32), residues: 264 loop : -1.43 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 53 HIS 0.005 0.002 HIS A 71 PHE 0.022 0.003 PHE B 208 TYR 0.015 0.002 TYR B 200 ARG 0.003 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 0.837 Fit side-chains REVERT: A 25 LEU cc_start: 0.9074 (mt) cc_final: 0.8771 (mt) REVERT: A 30 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6698 (mm-30) REVERT: A 81 GLN cc_start: 0.8038 (tt0) cc_final: 0.7754 (tt0) REVERT: A 85 ASN cc_start: 0.8588 (m110) cc_final: 0.8295 (m-40) REVERT: A 139 ARG cc_start: 0.8379 (mtm110) cc_final: 0.7828 (mtp85) REVERT: A 140 ILE cc_start: 0.8785 (pt) cc_final: 0.8420 (pt) REVERT: A 222 SER cc_start: 0.8721 (p) cc_final: 0.8229 (t) REVERT: A 308 LYS cc_start: 0.7830 (mttp) cc_final: 0.7463 (tttm) REVERT: A 353 LEU cc_start: 0.9041 (tp) cc_final: 0.8723 (tp) REVERT: A 396 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8131 (tm-30) REVERT: A 397 GLU cc_start: 0.7205 (pt0) cc_final: 0.6688 (mt-10) REVERT: A 450 GLN cc_start: 0.8877 (tp40) cc_final: 0.8558 (tp-100) REVERT: B 44 VAL cc_start: 0.8996 (p) cc_final: 0.8793 (m) REVERT: B 85 ASN cc_start: 0.8554 (m110) cc_final: 0.8342 (m-40) REVERT: B 93 THR cc_start: 0.8339 (t) cc_final: 0.8067 (p) REVERT: B 192 LYS cc_start: 0.7898 (tttt) cc_final: 0.7447 (ttmm) REVERT: B 222 SER cc_start: 0.8527 (p) cc_final: 0.8124 (t) REVERT: B 252 VAL cc_start: 0.9111 (p) cc_final: 0.8899 (m) REVERT: B 308 LYS cc_start: 0.7904 (mttp) cc_final: 0.7443 (tttm) REVERT: B 396 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8202 (tm-30) REVERT: B 397 GLU cc_start: 0.7094 (pt0) cc_final: 0.6768 (mt-10) REVERT: B 425 ILE cc_start: 0.8846 (pt) cc_final: 0.8392 (mt) REVERT: B 450 GLN cc_start: 0.8890 (tp40) cc_final: 0.8554 (tp-100) outliers start: 2 outliers final: 2 residues processed: 276 average time/residue: 0.2268 time to fit residues: 80.0157 Evaluate side-chains 187 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 370 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN ** A 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 ASN B 113 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7764 Z= 0.258 Angle : 0.559 6.615 10532 Z= 0.294 Chirality : 0.046 0.149 1174 Planarity : 0.004 0.051 1336 Dihedral : 6.354 45.212 1148 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.63 % Allowed : 15.91 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.31 (0.26), residues: 966 helix: 2.02 (0.30), residues: 278 sheet: 0.08 (0.34), residues: 256 loop : -0.91 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 98 HIS 0.006 0.002 HIS A 243 PHE 0.024 0.002 PHE B 208 TYR 0.015 0.002 TYR B 13 ARG 0.005 0.001 ARG B 268 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 191 time to evaluate : 0.777 Fit side-chains REVERT: A 139 ARG cc_start: 0.8148 (mtm110) cc_final: 0.7602 (mtp85) REVERT: A 140 ILE cc_start: 0.8672 (pt) cc_final: 0.8433 (pt) REVERT: A 222 SER cc_start: 0.8773 (p) cc_final: 0.8330 (t) REVERT: A 308 LYS cc_start: 0.7961 (mttp) cc_final: 0.7462 (tttm) REVERT: A 425 ILE cc_start: 0.8716 (pt) cc_final: 0.8298 (mt) REVERT: A 479 PHE cc_start: 0.8657 (m-80) cc_final: 0.8273 (m-80) REVERT: B 29 LYS cc_start: 0.8005 (mtpt) cc_final: 0.7721 (mttt) REVERT: B 44 VAL cc_start: 0.9091 (p) cc_final: 0.8879 (m) REVERT: B 91 GLU cc_start: 0.7703 (mp0) cc_final: 0.7494 (mp0) REVERT: B 139 ARG cc_start: 0.8355 (mtm110) cc_final: 0.7846 (mtp85) REVERT: B 222 SER cc_start: 0.8734 (p) cc_final: 0.8251 (t) REVERT: B 252 VAL cc_start: 0.8869 (p) cc_final: 0.8588 (m) REVERT: B 308 LYS cc_start: 0.7931 (mttp) cc_final: 0.7495 (tttm) REVERT: B 386 SER cc_start: 0.8738 (t) cc_final: 0.8289 (p) outliers start: 21 outliers final: 13 residues processed: 205 average time/residue: 0.1968 time to fit residues: 54.0944 Evaluate side-chains 178 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 165 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7764 Z= 0.242 Angle : 0.526 6.402 10532 Z= 0.275 Chirality : 0.045 0.148 1174 Planarity : 0.004 0.037 1336 Dihedral : 6.015 42.834 1148 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.14 % Allowed : 18.42 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.58 (0.27), residues: 966 helix: 2.33 (0.32), residues: 280 sheet: 0.11 (0.34), residues: 256 loop : -0.74 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 98 HIS 0.005 0.001 HIS A 243 PHE 0.017 0.002 PHE A 157 TYR 0.011 0.001 TYR A 358 ARG 0.003 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 0.854 Fit side-chains REVERT: A 12 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7196 (m-30) REVERT: A 49 LEU cc_start: 0.8586 (mp) cc_final: 0.8238 (mp) REVERT: A 139 ARG cc_start: 0.8147 (mtm110) cc_final: 0.7605 (mtp85) REVERT: A 157 PHE cc_start: 0.8769 (m-80) cc_final: 0.8482 (m-10) REVERT: A 222 SER cc_start: 0.8933 (p) cc_final: 0.8619 (t) REVERT: A 308 LYS cc_start: 0.8041 (mttp) cc_final: 0.7484 (tttm) REVERT: A 397 GLU cc_start: 0.7340 (pt0) cc_final: 0.7133 (mt-10) REVERT: A 425 ILE cc_start: 0.8773 (pt) cc_final: 0.8384 (mt) REVERT: A 479 PHE cc_start: 0.8733 (m-80) cc_final: 0.8223 (m-80) REVERT: B 12 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: B 29 LYS cc_start: 0.8045 (mtpt) cc_final: 0.7407 (mttt) REVERT: B 139 ARG cc_start: 0.8317 (mtm110) cc_final: 0.7587 (mtp85) REVERT: B 222 SER cc_start: 0.8904 (p) cc_final: 0.8515 (t) REVERT: B 252 VAL cc_start: 0.8702 (p) cc_final: 0.8452 (m) REVERT: B 308 LYS cc_start: 0.8051 (mttp) cc_final: 0.7520 (tttm) REVERT: B 386 SER cc_start: 0.8732 (t) cc_final: 0.8322 (p) REVERT: B 397 GLU cc_start: 0.7460 (pt0) cc_final: 0.7081 (mt-10) outliers start: 33 outliers final: 25 residues processed: 200 average time/residue: 0.1956 time to fit residues: 52.5043 Evaluate side-chains 200 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 173 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 0.0030 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7764 Z= 0.159 Angle : 0.472 7.530 10532 Z= 0.245 Chirality : 0.043 0.139 1174 Planarity : 0.003 0.032 1336 Dihedral : 5.650 41.197 1148 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.51 % Allowed : 20.05 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.87 (0.27), residues: 966 helix: 2.68 (0.32), residues: 276 sheet: 0.13 (0.33), residues: 246 loop : -0.50 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 98 HIS 0.004 0.001 HIS B 243 PHE 0.016 0.001 PHE B 157 TYR 0.011 0.001 TYR B 13 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 0.917 Fit side-chains REVERT: A 29 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7055 (mttt) REVERT: A 139 ARG cc_start: 0.8196 (mtm110) cc_final: 0.7641 (mtp85) REVERT: A 222 SER cc_start: 0.8989 (p) cc_final: 0.8781 (t) REVERT: A 250 GLN cc_start: 0.7879 (mt0) cc_final: 0.7671 (mm-40) REVERT: A 294 ASP cc_start: 0.7946 (t0) cc_final: 0.7701 (t0) REVERT: A 308 LYS cc_start: 0.8059 (mttp) cc_final: 0.7515 (tttm) REVERT: A 397 GLU cc_start: 0.7331 (pt0) cc_final: 0.6957 (mt-10) REVERT: A 425 ILE cc_start: 0.8739 (pt) cc_final: 0.8282 (mt) REVERT: A 479 PHE cc_start: 0.8720 (m-80) cc_final: 0.8169 (m-80) REVERT: B 29 LYS cc_start: 0.7875 (mtpt) cc_final: 0.7255 (mttt) REVERT: B 139 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7725 (mtp85) REVERT: B 150 LYS cc_start: 0.8161 (mttt) cc_final: 0.7741 (tptp) REVERT: B 222 SER cc_start: 0.8920 (p) cc_final: 0.8619 (t) REVERT: B 252 VAL cc_start: 0.8547 (p) cc_final: 0.8179 (m) REVERT: B 279 ILE cc_start: 0.8627 (mm) cc_final: 0.8426 (tp) REVERT: B 287 VAL cc_start: 0.9083 (t) cc_final: 0.8830 (m) REVERT: B 294 ASP cc_start: 0.7958 (t0) cc_final: 0.7687 (t0) REVERT: B 308 LYS cc_start: 0.8075 (mttp) cc_final: 0.7551 (tttm) REVERT: B 353 LEU cc_start: 0.8835 (tp) cc_final: 0.8566 (tp) REVERT: B 397 GLU cc_start: 0.7356 (pt0) cc_final: 0.7056 (mt-10) REVERT: B 425 ILE cc_start: 0.8830 (pt) cc_final: 0.8376 (mt) REVERT: B 479 PHE cc_start: 0.8619 (m-80) cc_final: 0.8394 (m-80) outliers start: 28 outliers final: 24 residues processed: 207 average time/residue: 0.1899 time to fit residues: 53.3567 Evaluate side-chains 205 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 145 ASN Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN B 243 HIS ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.080 7764 Z= 0.685 Angle : 0.845 8.697 10532 Z= 0.433 Chirality : 0.054 0.175 1174 Planarity : 0.005 0.039 1336 Dihedral : 7.382 47.071 1148 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 7.64 % Allowed : 19.92 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.38 (0.26), residues: 966 helix: 1.38 (0.31), residues: 278 sheet: -0.56 (0.34), residues: 226 loop : -1.10 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 53 HIS 0.011 0.004 HIS A 243 PHE 0.023 0.003 PHE B 208 TYR 0.019 0.003 TYR A 358 ARG 0.004 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 178 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6971 (tt0) REVERT: A 149 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6512 (tm-30) REVERT: A 205 CYS cc_start: 0.8136 (m) cc_final: 0.7831 (m) REVERT: A 222 SER cc_start: 0.9152 (p) cc_final: 0.8823 (t) REVERT: A 243 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7324 (t70) REVERT: A 257 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: A 308 LYS cc_start: 0.8223 (mttp) cc_final: 0.7815 (tttm) REVERT: B 12 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7150 (m-30) REVERT: B 205 CYS cc_start: 0.8062 (m) cc_final: 0.7810 (m) REVERT: B 222 SER cc_start: 0.9112 (p) cc_final: 0.8826 (t) REVERT: B 252 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8410 (m) REVERT: B 308 LYS cc_start: 0.8215 (mttp) cc_final: 0.7452 (tttm) REVERT: B 363 VAL cc_start: 0.9231 (t) cc_final: 0.9017 (m) REVERT: B 447 GLU cc_start: 0.8262 (mp0) cc_final: 0.7710 (mp0) outliers start: 61 outliers final: 38 residues processed: 214 average time/residue: 0.1622 time to fit residues: 48.7350 Evaluate side-chains 215 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 171 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 456 LEU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 243 HIS Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 329 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 9.9990 chunk 48 optimal weight: 1.0980 chunk 89 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 239 HIS B 243 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7764 Z= 0.187 Angle : 0.535 8.169 10532 Z= 0.276 Chirality : 0.044 0.166 1174 Planarity : 0.003 0.031 1336 Dihedral : 6.118 43.610 1148 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.51 % Allowed : 23.93 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.20 (0.27), residues: 966 helix: 2.19 (0.32), residues: 278 sheet: -0.35 (0.34), residues: 230 loop : -0.90 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 407 HIS 0.007 0.002 HIS B 243 PHE 0.013 0.002 PHE B 208 TYR 0.014 0.001 TYR B 13 ARG 0.004 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 0.887 Fit side-chains REVERT: A 81 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.7091 (tt0) REVERT: A 243 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.6899 (t70) REVERT: A 250 GLN cc_start: 0.8095 (mt0) cc_final: 0.7877 (mm-40) REVERT: A 308 LYS cc_start: 0.8102 (mttp) cc_final: 0.7608 (tmtt) REVERT: A 319 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8426 (m) REVERT: B 29 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7343 (mttt) REVERT: B 205 CYS cc_start: 0.7809 (m) cc_final: 0.7367 (m) REVERT: B 254 ILE cc_start: 0.8740 (pt) cc_final: 0.8407 (mm) REVERT: B 308 LYS cc_start: 0.8149 (mttp) cc_final: 0.7740 (tmtt) REVERT: B 319 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8351 (m) REVERT: B 386 SER cc_start: 0.8776 (t) cc_final: 0.8301 (p) REVERT: B 425 ILE cc_start: 0.8719 (pt) cc_final: 0.8217 (mt) outliers start: 36 outliers final: 27 residues processed: 213 average time/residue: 0.1701 time to fit residues: 50.7524 Evaluate side-chains 208 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 81 GLN Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7764 Z= 0.292 Angle : 0.580 8.454 10532 Z= 0.298 Chirality : 0.046 0.162 1174 Planarity : 0.004 0.031 1336 Dihedral : 6.241 43.785 1147 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.39 % Allowed : 23.68 % Favored : 70.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.09 (0.27), residues: 966 helix: 2.23 (0.32), residues: 276 sheet: -0.52 (0.34), residues: 234 loop : -0.98 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 98 HIS 0.005 0.002 HIS A 239 PHE 0.016 0.002 PHE B 208 TYR 0.013 0.001 TYR B 13 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 191 time to evaluate : 0.843 Fit side-chains REVERT: A 163 GLU cc_start: 0.7492 (pt0) cc_final: 0.7173 (pm20) REVERT: A 257 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6790 (mt-10) REVERT: A 308 LYS cc_start: 0.8114 (mttp) cc_final: 0.7601 (tmtt) REVERT: A 319 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8282 (m) REVERT: A 334 ASP cc_start: 0.7682 (p0) cc_final: 0.7136 (p0) REVERT: A 386 SER cc_start: 0.8726 (t) cc_final: 0.8453 (p) REVERT: A 425 ILE cc_start: 0.8863 (pt) cc_final: 0.8438 (mt) REVERT: B 29 LYS cc_start: 0.7749 (mtpt) cc_final: 0.7370 (mttt) REVERT: B 205 CYS cc_start: 0.8040 (m) cc_final: 0.7765 (m) REVERT: B 280 ILE cc_start: 0.7360 (pt) cc_final: 0.6768 (tt) REVERT: B 288 MET cc_start: 0.8072 (ttp) cc_final: 0.7668 (mtp) REVERT: B 308 LYS cc_start: 0.8168 (mttp) cc_final: 0.7737 (tmtt) REVERT: B 319 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8380 (m) REVERT: B 425 ILE cc_start: 0.8742 (pt) cc_final: 0.8233 (mt) outliers start: 43 outliers final: 35 residues processed: 217 average time/residue: 0.1734 time to fit residues: 52.1808 Evaluate side-chains 228 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 190 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 243 HIS Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 80 optimal weight: 0.0270 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7764 Z= 0.214 Angle : 0.553 8.289 10532 Z= 0.283 Chirality : 0.045 0.159 1174 Planarity : 0.003 0.030 1336 Dihedral : 6.077 42.583 1147 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 5.39 % Allowed : 24.56 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.19 (0.27), residues: 966 helix: 2.27 (0.32), residues: 278 sheet: -0.53 (0.34), residues: 232 loop : -0.86 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 98 HIS 0.005 0.001 HIS A 96 PHE 0.016 0.002 PHE B 208 TYR 0.011 0.001 TYR B 13 ARG 0.005 0.000 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 198 time to evaluate : 0.911 Fit side-chains REVERT: A 29 LYS cc_start: 0.7930 (mtpt) cc_final: 0.7482 (mttt) REVERT: A 163 GLU cc_start: 0.7492 (pt0) cc_final: 0.7050 (pm20) REVERT: A 308 LYS cc_start: 0.8095 (mttp) cc_final: 0.7595 (tmtt) REVERT: A 319 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8473 (m) REVERT: A 334 ASP cc_start: 0.7701 (p0) cc_final: 0.7152 (p0) REVERT: A 386 SER cc_start: 0.8708 (t) cc_final: 0.8397 (p) REVERT: A 425 ILE cc_start: 0.8827 (pt) cc_final: 0.8403 (mt) REVERT: B 29 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7314 (mttt) REVERT: B 76 LEU cc_start: 0.9307 (mp) cc_final: 0.9022 (mm) REVERT: B 163 GLU cc_start: 0.7452 (pt0) cc_final: 0.6932 (pm20) REVERT: B 224 LEU cc_start: 0.8651 (mm) cc_final: 0.8448 (mt) REVERT: B 254 ILE cc_start: 0.8654 (pt) cc_final: 0.8409 (mm) REVERT: B 280 ILE cc_start: 0.7245 (pt) cc_final: 0.6617 (tt) REVERT: B 288 MET cc_start: 0.7865 (ttp) cc_final: 0.7546 (mtp) REVERT: B 308 LYS cc_start: 0.8122 (mttp) cc_final: 0.7626 (tmtt) REVERT: B 319 THR cc_start: 0.8589 (OUTLIER) cc_final: 0.8252 (m) REVERT: B 334 ASP cc_start: 0.7492 (p0) cc_final: 0.6860 (p0) REVERT: B 356 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7374 (ttm-80) REVERT: B 386 SER cc_start: 0.8760 (t) cc_final: 0.8508 (p) REVERT: B 425 ILE cc_start: 0.8899 (pt) cc_final: 0.8431 (mt) outliers start: 43 outliers final: 32 residues processed: 222 average time/residue: 0.1809 time to fit residues: 55.1645 Evaluate side-chains 226 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 192 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7764 Z= 0.179 Angle : 0.524 8.031 10532 Z= 0.271 Chirality : 0.045 0.163 1174 Planarity : 0.004 0.034 1336 Dihedral : 5.855 41.709 1146 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.26 % Allowed : 25.94 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.36 (0.28), residues: 966 helix: 2.53 (0.32), residues: 274 sheet: -0.49 (0.34), residues: 232 loop : -0.76 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 98 HIS 0.006 0.001 HIS B 96 PHE 0.017 0.002 PHE B 208 TYR 0.013 0.001 TYR A 358 ARG 0.007 0.000 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 198 time to evaluate : 0.889 Fit side-chains REVERT: A 29 LYS cc_start: 0.7807 (mtpt) cc_final: 0.7189 (mttt) REVERT: A 39 MET cc_start: 0.8825 (ppp) cc_final: 0.8493 (ppp) REVERT: A 149 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.6230 (tm-30) REVERT: A 163 GLU cc_start: 0.7372 (pt0) cc_final: 0.7072 (pm20) REVERT: A 294 ASP cc_start: 0.8030 (t0) cc_final: 0.7153 (p0) REVERT: A 308 LYS cc_start: 0.8096 (mttp) cc_final: 0.7608 (tmtt) REVERT: A 319 THR cc_start: 0.8618 (OUTLIER) cc_final: 0.8239 (m) REVERT: A 334 ASP cc_start: 0.7642 (p0) cc_final: 0.7172 (p0) REVERT: A 358 TYR cc_start: 0.7442 (m-80) cc_final: 0.7045 (m-80) REVERT: A 386 SER cc_start: 0.8721 (t) cc_final: 0.8406 (p) REVERT: A 425 ILE cc_start: 0.8793 (pt) cc_final: 0.8337 (mt) REVERT: A 479 PHE cc_start: 0.8631 (m-80) cc_final: 0.8329 (m-80) REVERT: B 13 TYR cc_start: 0.6281 (m-10) cc_final: 0.5948 (m-10) REVERT: B 29 LYS cc_start: 0.7758 (mtpt) cc_final: 0.7262 (mttt) REVERT: B 39 MET cc_start: 0.8625 (ppp) cc_final: 0.8348 (ppp) REVERT: B 76 LEU cc_start: 0.9320 (mp) cc_final: 0.8993 (mm) REVERT: B 150 LYS cc_start: 0.8284 (tptp) cc_final: 0.7880 (mttt) REVERT: B 163 GLU cc_start: 0.7302 (pt0) cc_final: 0.7017 (pm20) REVERT: B 280 ILE cc_start: 0.7146 (pt) cc_final: 0.6498 (tt) REVERT: B 308 LYS cc_start: 0.8118 (mttp) cc_final: 0.7639 (tmtt) REVERT: B 319 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8241 (m) REVERT: B 334 ASP cc_start: 0.7441 (p0) cc_final: 0.6904 (p0) REVERT: B 425 ILE cc_start: 0.8872 (pt) cc_final: 0.8427 (mt) outliers start: 34 outliers final: 27 residues processed: 220 average time/residue: 0.1641 time to fit residues: 50.2172 Evaluate side-chains 221 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 191 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 60 optimal weight: 0.0870 chunk 81 optimal weight: 7.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7764 Z= 0.175 Angle : 0.521 7.775 10532 Z= 0.270 Chirality : 0.044 0.158 1174 Planarity : 0.003 0.031 1336 Dihedral : 5.743 40.801 1146 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.01 % Allowed : 26.07 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.43 (0.28), residues: 966 helix: 2.50 (0.32), residues: 276 sheet: -0.41 (0.34), residues: 230 loop : -0.70 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 98 HIS 0.006 0.001 HIS A 96 PHE 0.017 0.002 PHE B 208 TYR 0.011 0.001 TYR A 13 ARG 0.008 0.000 ARG B 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7673 (mtpt) cc_final: 0.7242 (mttt) REVERT: A 39 MET cc_start: 0.8750 (ppp) cc_final: 0.8494 (ppp) REVERT: A 76 LEU cc_start: 0.9210 (mp) cc_final: 0.8941 (mm) REVERT: A 86 TYR cc_start: 0.9014 (m-80) cc_final: 0.8394 (m-80) REVERT: A 149 GLU cc_start: 0.6537 (OUTLIER) cc_final: 0.6185 (tm-30) REVERT: A 163 GLU cc_start: 0.7420 (pt0) cc_final: 0.6997 (pm20) REVERT: A 308 LYS cc_start: 0.8087 (mttp) cc_final: 0.7585 (tmtt) REVERT: A 319 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8205 (m) REVERT: A 334 ASP cc_start: 0.7604 (p0) cc_final: 0.7099 (p0) REVERT: A 425 ILE cc_start: 0.8769 (pt) cc_final: 0.8352 (mt) REVERT: A 479 PHE cc_start: 0.8600 (m-80) cc_final: 0.8300 (m-80) REVERT: B 29 LYS cc_start: 0.7668 (mtpt) cc_final: 0.7233 (mttt) REVERT: B 86 TYR cc_start: 0.8797 (m-80) cc_final: 0.8390 (m-80) REVERT: B 150 LYS cc_start: 0.8342 (tptp) cc_final: 0.7924 (mttt) REVERT: B 163 GLU cc_start: 0.7421 (pt0) cc_final: 0.7011 (pm20) REVERT: B 280 ILE cc_start: 0.7140 (pt) cc_final: 0.6438 (tt) REVERT: B 294 ASP cc_start: 0.8010 (t0) cc_final: 0.7179 (p0) REVERT: B 308 LYS cc_start: 0.8135 (mttp) cc_final: 0.7646 (tmtt) REVERT: B 319 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8177 (m) REVERT: B 334 ASP cc_start: 0.7417 (p0) cc_final: 0.6890 (p0) REVERT: B 425 ILE cc_start: 0.8857 (pt) cc_final: 0.8424 (mt) outliers start: 32 outliers final: 29 residues processed: 211 average time/residue: 0.1738 time to fit residues: 50.9617 Evaluate side-chains 220 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 269 VAL Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 VAL Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 313 THR Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 492 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.131216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.112743 restraints weight = 9229.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.113332 restraints weight = 9005.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.114255 restraints weight = 7415.600| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 7764 Z= 0.379 Angle : 0.632 7.450 10532 Z= 0.327 Chirality : 0.048 0.227 1174 Planarity : 0.004 0.054 1336 Dihedral : 6.480 42.877 1146 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 5.14 % Allowed : 25.19 % Favored : 69.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.06 (0.28), residues: 966 helix: 2.13 (0.32), residues: 278 sheet: -0.78 (0.35), residues: 222 loop : -0.80 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 98 HIS 0.007 0.002 HIS A 403 PHE 0.019 0.002 PHE B 208 TYR 0.016 0.002 TYR A 13 ARG 0.010 0.001 ARG B 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1787.52 seconds wall clock time: 33 minutes 5.09 seconds (1985.09 seconds total)