Starting phenix.real_space_refine on Fri Jul 19 10:45:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/07_2024/7x1r_32947_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/07_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_32947/07_2024/7x1r_32947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/07_2024/7x1r_32947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/07_2024/7x1r_32947_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/07_2024/7x1r_32947_neut.cif" } 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 4.65, per 1000 atoms: 0.61 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 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... Secondary structure from input PDB file: 30 helices and 12 sheets defined 36.7% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 21 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 56 through 63 removed outlier: 4.346A pdb=" N VAL A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 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 97 through 123 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 180 through 184 removed outlier: 4.188A pdb=" N PHE A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 184' Processing helix chain 'A' and resid 199 through 212 Processing helix chain 'A' and resid 229 through 243 Processing helix chain 'A' and resid 342 through 359 Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 408 through 412 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 444 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 461 through 468 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'B' and resid 21 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 56 through 63 removed outlier: 4.347A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 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 97 through 123 Processing helix chain 'B' and resid 172 through 177 Processing helix chain 'B' and resid 180 through 184 removed outlier: 4.188A pdb=" N PHE B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 184' Processing helix chain 'B' and resid 199 through 212 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 342 through 359 Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 408 through 412 Processing helix chain 'B' and resid 430 through 432 No H-bonds generated for 'chain 'B' and resid 430 through 432' Processing helix chain 'B' and resid 444 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 461 through 468 Processing helix chain 'B' and resid 474 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET A 39 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 15 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU A 41 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 17 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP A 14 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU A 158 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 16 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG A 139 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE A 135 " --> pdb=" O ARG A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET A 39 " --> pdb=" O TYR A 13 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LEU A 15 " --> pdb=" O MET A 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU A 41 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 17 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP A 14 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N LEU A 158 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 16 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N TYR A 330 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N PHE A 157 " --> pdb=" O TYR A 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 163 through 165 Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179 removed outlier: 6.828A pdb=" N ILE A 178 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 251 through 260 removed outlier: 5.997A pdb=" N GLN A 272 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG A 266 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 372 through 374 removed outlier: 5.929A pdb=" N VAL A 435 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN A 428 " --> pdb=" O VAL A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET B 39 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 15 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 41 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 17 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 14 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 158 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 16 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ARG B 139 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE B 135 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 126 through 128 removed outlier: 7.235A pdb=" N MET B 39 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LEU B 15 " --> pdb=" O MET B 39 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 41 " --> pdb=" O LEU B 15 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 17 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASP B 14 " --> pdb=" O ARG B 156 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 158 " --> pdb=" O ASP B 14 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 16 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N TYR B 330 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE B 157 " --> pdb=" O TYR B 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 163 through 165 Processing sheet with id=AB1, first strand: chain 'B' and resid 178 through 179 removed outlier: 6.829A pdb=" N ILE B 178 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 251 through 260 removed outlier: 5.997A pdb=" N GLN B 272 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ARG B 266 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 372 through 374 removed outlier: 5.929A pdb=" N VAL B 435 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASN B 428 " --> pdb=" O VAL B 435 " (cutoff:3.500A) 342 hydrogen bonds defined for protein. 948 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: 2.49 Time building geometry restraints manager: 3.38 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: 969 2.74 - 3.28: 7362 3.28 - 3.82: 12429 3.82 - 4.36: 14855 4.36 - 4.90: 25607 Nonbonded interactions: 61222 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 61217 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: 0.060 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.120 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- 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= 0.473 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 : 0.826 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: 0.2349 time to fit residues: 83.4173 Evaluate side-chains 187 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.809 ------------------------------------------------------------------------------- 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: 0.2980 chunk 72 optimal weight: 10.0000 chunk 40 optimal weight: 0.0870 chunk 24 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.4764 ------------------------------------------------------------------------------- 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 144 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7764 Z= 0.207 Angle : 0.560 6.898 10532 Z= 0.298 Chirality : 0.046 0.150 1174 Planarity : 0.004 0.051 1336 Dihedral : 6.274 44.131 1148 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.13 % Allowed : 15.66 % Favored : 82.21 % 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: 0.23 (0.26), residues: 966 helix: 1.91 (0.29), residues: 294 sheet: 0.02 (0.33), residues: 256 loop : -1.02 (0.27), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 98 HIS 0.005 0.002 HIS B 96 PHE 0.026 0.002 PHE B 208 TYR 0.016 0.001 TYR B 13 ARG 0.004 0.000 ARG A 121 *********************** 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 218 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 0.764 Fit side-chains REVERT: A 157 PHE cc_start: 0.8555 (m-80) cc_final: 0.8338 (m-10) REVERT: A 222 SER cc_start: 0.8701 (p) cc_final: 0.8272 (t) REVERT: A 308 LYS cc_start: 0.7910 (mttp) cc_final: 0.7446 (tttm) REVERT: A 397 GLU cc_start: 0.7387 (pt0) cc_final: 0.7042 (pt0) REVERT: A 403 HIS cc_start: 0.8691 (p90) cc_final: 0.8342 (p-80) REVERT: A 479 PHE cc_start: 0.8594 (m-80) cc_final: 0.8233 (m-80) REVERT: B 29 LYS cc_start: 0.7938 (mtpt) cc_final: 0.7678 (mttt) REVERT: B 44 VAL cc_start: 0.9087 (p) cc_final: 0.8864 (m) REVERT: B 139 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7771 (mtp85) REVERT: B 157 PHE cc_start: 0.8479 (m-80) cc_final: 0.8247 (m-10) REVERT: B 192 LYS cc_start: 0.7965 (tttt) cc_final: 0.7551 (ttmm) REVERT: B 222 SER cc_start: 0.8648 (p) cc_final: 0.8164 (t) REVERT: B 252 VAL cc_start: 0.8870 (p) cc_final: 0.8654 (m) REVERT: B 308 LYS cc_start: 0.7865 (mttp) cc_final: 0.7452 (tttm) REVERT: B 386 SER cc_start: 0.8711 (t) cc_final: 0.8261 (p) REVERT: B 450 GLN cc_start: 0.8720 (tp40) cc_final: 0.8354 (tp-100) outliers start: 17 outliers final: 10 residues processed: 213 average time/residue: 0.1815 time to fit residues: 52.6334 Evaluate side-chains 188 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 178 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 436 VAL 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: 8.9990 chunk 27 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 0.0770 chunk 86 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7764 Z= 0.233 Angle : 0.553 6.649 10532 Z= 0.293 Chirality : 0.046 0.156 1174 Planarity : 0.004 0.038 1336 Dihedral : 5.994 42.296 1148 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.64 % Allowed : 16.42 % Favored : 78.95 % 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: 0.52 (0.27), residues: 966 helix: 2.26 (0.31), residues: 294 sheet: 0.04 (0.32), residues: 256 loop : -0.85 (0.28), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 53 HIS 0.004 0.001 HIS B 108 PHE 0.020 0.002 PHE A 208 TYR 0.011 0.001 TYR B 13 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 225 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 0.875 Fit side-chains REVERT: A 222 SER cc_start: 0.8872 (p) cc_final: 0.8522 (t) REVERT: A 308 LYS cc_start: 0.8030 (mttp) cc_final: 0.7511 (tttm) REVERT: A 397 GLU cc_start: 0.7244 (pt0) cc_final: 0.7040 (mt-10) REVERT: A 403 HIS cc_start: 0.8722 (p90) cc_final: 0.8285 (p90) REVERT: A 479 PHE cc_start: 0.8643 (m-80) cc_final: 0.8265 (m-80) REVERT: B 12 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: B 44 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8751 (m) REVERT: B 139 ARG cc_start: 0.8418 (mtm110) cc_final: 0.7658 (mtp85) REVERT: B 157 PHE cc_start: 0.8616 (m-80) cc_final: 0.8318 (m-10) REVERT: B 222 SER cc_start: 0.8883 (p) cc_final: 0.8483 (t) REVERT: B 252 VAL cc_start: 0.8719 (p) cc_final: 0.8421 (m) REVERT: B 289 LEU cc_start: 0.8902 (mt) cc_final: 0.8566 (mp) REVERT: B 308 LYS cc_start: 0.8017 (mttp) cc_final: 0.7542 (tttm) outliers start: 37 outliers final: 29 residues processed: 211 average time/residue: 0.1859 time to fit residues: 53.0440 Evaluate side-chains 202 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE 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 161 THR Chi-restraints excluded: chain A residue 201 VAL 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 44 VAL 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 201 VAL Chi-restraints excluded: chain B residue 245 ILE 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 492 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 5.9990 chunk 65 optimal weight: 0.0470 chunk 45 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 7.9990 overall best weight: 2.7684 ------------------------------------------------------------------------------- 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** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7764 Z= 0.296 Angle : 0.591 8.000 10532 Z= 0.308 Chirality : 0.046 0.147 1174 Planarity : 0.004 0.032 1336 Dihedral : 6.088 41.358 1148 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 6.02 % Allowed : 18.92 % Favored : 75.06 % 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: 0.41 (0.27), residues: 966 helix: 2.34 (0.31), residues: 282 sheet: -0.11 (0.32), residues: 258 loop : -0.90 (0.28), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 88 HIS 0.005 0.002 HIS B 138 PHE 0.021 0.002 PHE B 208 TYR 0.013 0.002 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 230 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 0.847 Fit side-chains REVERT: A 222 SER cc_start: 0.8951 (p) cc_final: 0.8698 (t) REVERT: A 257 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6824 (mt-10) REVERT: A 294 ASP cc_start: 0.8028 (t0) cc_final: 0.7753 (t0) REVERT: A 308 LYS cc_start: 0.8117 (mttp) cc_final: 0.7506 (tttm) REVERT: A 397 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7115 (mt-10) REVERT: A 403 HIS cc_start: 0.8584 (p90) cc_final: 0.8084 (p90) REVERT: B 15 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8998 (tp) REVERT: B 139 ARG cc_start: 0.8134 (mtm110) cc_final: 0.7677 (mtp85) REVERT: B 205 CYS cc_start: 0.8020 (m) cc_final: 0.7778 (m) REVERT: B 222 SER cc_start: 0.9000 (p) cc_final: 0.8701 (t) REVERT: B 252 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8346 (m) REVERT: B 289 LEU cc_start: 0.8951 (mt) cc_final: 0.8565 (mp) REVERT: B 294 ASP cc_start: 0.8010 (t0) cc_final: 0.7715 (t0) REVERT: B 308 LYS cc_start: 0.8081 (mttp) cc_final: 0.7489 (tttm) outliers start: 48 outliers final: 30 residues processed: 210 average time/residue: 0.1760 time to fit residues: 50.8193 Evaluate side-chains 207 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 173 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 118 VAL 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 257 GLU Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 397 GLU 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 477 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 15 LEU 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 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 370 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain B residue 436 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7764 Z= 0.423 Angle : 0.678 10.239 10532 Z= 0.352 Chirality : 0.048 0.150 1174 Planarity : 0.004 0.032 1336 Dihedral : 6.569 43.960 1148 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 6.02 % Allowed : 21.05 % Favored : 72.93 % 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: -0.00 (0.27), residues: 966 helix: 2.03 (0.31), residues: 280 sheet: -0.43 (0.32), residues: 258 loop : -1.09 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 88 HIS 0.007 0.003 HIS B 403 PHE 0.020 0.002 PHE B 208 TYR 0.013 0.002 TYR A 13 ARG 0.003 0.001 ARG A 84 *********************** 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 224 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 176 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 140 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8186 (pt) REVERT: A 149 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.6621 (tm-30) REVERT: A 222 SER cc_start: 0.9089 (p) cc_final: 0.8840 (t) REVERT: A 257 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: A 308 LYS cc_start: 0.8178 (mttp) cc_final: 0.7672 (tttm) REVERT: B 15 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8827 (tt) REVERT: B 81 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: B 139 ARG cc_start: 0.8210 (mtm110) cc_final: 0.7686 (mtp85) REVERT: B 222 SER cc_start: 0.9107 (p) cc_final: 0.8857 (t) REVERT: B 252 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8365 (m) REVERT: B 308 LYS cc_start: 0.8176 (mttp) cc_final: 0.7711 (tttm) REVERT: B 425 ILE cc_start: 0.8592 (pt) cc_final: 0.8320 (mt) REVERT: B 433 GLU cc_start: 0.8429 (mp0) cc_final: 0.8162 (pm20) outliers start: 48 outliers final: 31 residues processed: 210 average time/residue: 0.1744 time to fit residues: 50.5234 Evaluate side-chains 208 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 171 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 112 LEU 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 201 VAL 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 370 VAL Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 477 GLU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 118 VAL 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 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 412 THR Chi-restraints excluded: chain B residue 480 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: 8.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7764 Z= 0.193 Angle : 0.545 8.802 10532 Z= 0.284 Chirality : 0.045 0.150 1174 Planarity : 0.003 0.032 1336 Dihedral : 5.907 40.438 1148 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 5.14 % Allowed : 21.80 % Favored : 73.06 % 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: 0.25 (0.27), residues: 966 helix: 2.21 (0.31), residues: 284 sheet: -0.35 (0.32), residues: 258 loop : -0.89 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 407 HIS 0.004 0.001 HIS B 243 PHE 0.027 0.002 PHE B 208 TYR 0.011 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 240 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 76 LEU cc_start: 0.9325 (mp) cc_final: 0.9108 (mm) REVERT: A 149 GLU cc_start: 0.6692 (OUTLIER) cc_final: 0.6451 (tm-30) REVERT: A 205 CYS cc_start: 0.8024 (m) cc_final: 0.7520 (m) REVERT: A 257 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: A 294 ASP cc_start: 0.8176 (t0) cc_final: 0.7507 (p0) REVERT: A 308 LYS cc_start: 0.8094 (mttp) cc_final: 0.7611 (tmtt) REVERT: A 319 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8257 (m) REVERT: A 403 HIS cc_start: 0.8415 (p90) cc_final: 0.8160 (p90) REVERT: A 444 ASN cc_start: 0.8417 (m-40) cc_final: 0.8215 (m-40) REVERT: A 447 GLU cc_start: 0.8162 (mp0) cc_final: 0.7718 (mp0) REVERT: A 479 PHE cc_start: 0.8687 (m-80) cc_final: 0.8426 (m-80) REVERT: B 81 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: B 139 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7671 (mtp85) REVERT: B 150 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7758 (tptt) REVERT: B 222 SER cc_start: 0.9084 (p) cc_final: 0.8870 (t) REVERT: B 294 ASP cc_start: 0.8118 (t0) cc_final: 0.7461 (p0) REVERT: B 308 LYS cc_start: 0.8134 (mttp) cc_final: 0.7728 (tmtt) outliers start: 41 outliers final: 30 residues processed: 225 average time/residue: 0.1639 time to fit residues: 51.6268 Evaluate side-chains 218 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE 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 243 HIS Chi-restraints excluded: chain A residue 257 GLU 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 426 ILE 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 80 LEU Chi-restraints excluded: chain B residue 81 GLN 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 243 HIS 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 370 VAL Chi-restraints excluded: chain B residue 412 THR 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 492 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS B 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4135 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= 0.192 Angle : 0.552 8.765 10532 Z= 0.285 Chirality : 0.045 0.147 1174 Planarity : 0.004 0.030 1336 Dihedral : 5.735 39.835 1147 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.01 % Allowed : 22.68 % Favored : 72.31 % 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: 0.33 (0.27), residues: 966 helix: 2.29 (0.31), residues: 284 sheet: -0.28 (0.32), residues: 258 loop : -0.87 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 88 HIS 0.006 0.002 HIS B 243 PHE 0.026 0.002 PHE A 208 TYR 0.016 0.001 TYR A 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: 40 poor density : 194 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7447 (t70) cc_final: 0.7053 (t70) REVERT: A 76 LEU cc_start: 0.9276 (mp) cc_final: 0.9015 (mm) REVERT: A 149 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6389 (tm-30) REVERT: A 163 GLU cc_start: 0.7488 (pt0) cc_final: 0.7102 (pm20) REVERT: A 257 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6875 (mt-10) REVERT: A 294 ASP cc_start: 0.8163 (t0) cc_final: 0.7433 (p0) REVERT: A 308 LYS cc_start: 0.8089 (mttp) cc_final: 0.7617 (tmtt) REVERT: A 319 THR cc_start: 0.8641 (OUTLIER) cc_final: 0.8239 (m) REVERT: A 334 ASP cc_start: 0.7758 (p0) cc_final: 0.7103 (p0) REVERT: A 403 HIS cc_start: 0.8413 (p90) cc_final: 0.8090 (p90) REVERT: A 479 PHE cc_start: 0.8655 (m-80) cc_final: 0.8373 (m-80) REVERT: B 70 MET cc_start: 0.7506 (mtp) cc_final: 0.7136 (mtp) REVERT: B 139 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7679 (mtp85) REVERT: B 150 LYS cc_start: 0.8051 (mtmt) cc_final: 0.7772 (tptt) REVERT: B 163 GLU cc_start: 0.7431 (pt0) cc_final: 0.7137 (pm20) REVERT: B 294 ASP cc_start: 0.8129 (t0) cc_final: 0.7410 (p0) REVERT: B 308 LYS cc_start: 0.8095 (mttp) cc_final: 0.7716 (tmtt) REVERT: B 319 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8206 (m) REVERT: B 334 ASP cc_start: 0.7697 (p0) cc_final: 0.7060 (p0) outliers start: 40 outliers final: 30 residues processed: 217 average time/residue: 0.1709 time to fit residues: 51.2205 Evaluate side-chains 216 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 182 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE 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 201 VAL 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 412 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 477 GLU 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 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 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 332 ILE 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 480 THR Chi-restraints excluded: chain B residue 481 THR 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: 9.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 88 optimal weight: 0.4980 chunk 80 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN B 444 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7764 Z= 0.241 Angle : 0.572 10.173 10532 Z= 0.296 Chirality : 0.045 0.157 1174 Planarity : 0.004 0.035 1336 Dihedral : 5.836 40.746 1147 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.89 % Allowed : 22.18 % Favored : 71.93 % 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: 0.31 (0.27), residues: 966 helix: 2.34 (0.31), residues: 282 sheet: -0.29 (0.32), residues: 258 loop : -0.92 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 88 HIS 0.003 0.001 HIS B 108 PHE 0.025 0.002 PHE B 208 TYR 0.014 0.001 TYR A 13 ARG 0.006 0.000 ARG A 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 240 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 193 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8099 (mtm110) cc_final: 0.7789 (mtp85) REVERT: A 149 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6343 (tm-30) REVERT: A 163 GLU cc_start: 0.7538 (pt0) cc_final: 0.7069 (pm20) REVERT: A 205 CYS cc_start: 0.8067 (m) cc_final: 0.7673 (m) REVERT: A 308 LYS cc_start: 0.8114 (mttp) cc_final: 0.7586 (tmtt) REVERT: A 319 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8263 (m) REVERT: A 334 ASP cc_start: 0.7801 (p0) cc_final: 0.7149 (p0) REVERT: A 444 ASN cc_start: 0.8419 (m110) cc_final: 0.8152 (m-40) REVERT: A 447 GLU cc_start: 0.8176 (mp0) cc_final: 0.7741 (mp0) REVERT: B 42 ASP cc_start: 0.7486 (t70) cc_final: 0.7074 (t70) REVERT: B 76 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8676 (mp) REVERT: B 139 ARG cc_start: 0.8149 (mtm110) cc_final: 0.7674 (mtp85) REVERT: B 163 GLU cc_start: 0.7494 (pt0) cc_final: 0.7129 (pm20) REVERT: B 294 ASP cc_start: 0.8148 (t0) cc_final: 0.7456 (p0) REVERT: B 308 LYS cc_start: 0.8071 (mttp) cc_final: 0.7617 (tmtt) REVERT: B 319 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8216 (m) REVERT: B 334 ASP cc_start: 0.7738 (p0) cc_final: 0.7191 (p0) REVERT: B 425 ILE cc_start: 0.8558 (pt) cc_final: 0.8321 (mt) outliers start: 47 outliers final: 33 residues processed: 218 average time/residue: 0.1810 time to fit residues: 53.9464 Evaluate side-chains 222 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 185 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE 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 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 412 THR Chi-restraints excluded: chain A residue 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 477 GLU 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 76 LEU 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 332 ILE 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 492 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 88 optimal weight: 0.0870 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 77 optimal weight: 0.0270 chunk 81 optimal weight: 0.0670 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 overall best weight: 0.2954 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7764 Z= 0.157 Angle : 0.551 8.820 10532 Z= 0.284 Chirality : 0.045 0.164 1174 Planarity : 0.003 0.031 1336 Dihedral : 5.469 37.180 1146 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.38 % Allowed : 25.44 % Favored : 71.18 % 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: 0.62 (0.27), residues: 966 helix: 2.55 (0.31), residues: 282 sheet: -0.07 (0.33), residues: 244 loop : -0.71 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 88 HIS 0.005 0.001 HIS B 96 PHE 0.031 0.002 PHE B 208 TYR 0.009 0.001 TYR A 13 ARG 0.008 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 237 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 210 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.6209 (m) cc_final: 0.5844 (m) REVERT: A 76 LEU cc_start: 0.9157 (mp) cc_final: 0.8775 (mm) REVERT: A 139 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7789 (mtp85) REVERT: A 149 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6191 (tm-30) REVERT: A 150 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7564 (tptp) REVERT: A 163 GLU cc_start: 0.7486 (pt0) cc_final: 0.7080 (pm20) REVERT: A 294 ASP cc_start: 0.8252 (t0) cc_final: 0.7657 (p0) REVERT: A 308 LYS cc_start: 0.8097 (mttp) cc_final: 0.7604 (tmtt) REVERT: A 319 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8080 (m) REVERT: A 334 ASP cc_start: 0.7596 (p0) cc_final: 0.6858 (p0) REVERT: A 362 THR cc_start: 0.7881 (m) cc_final: 0.7288 (t) REVERT: A 403 HIS cc_start: 0.8296 (p90) cc_final: 0.8049 (p90) REVERT: A 479 PHE cc_start: 0.8391 (m-80) cc_final: 0.8179 (m-80) REVERT: B 42 ASP cc_start: 0.7332 (t70) cc_final: 0.6866 (t70) REVERT: B 76 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8522 (mp) REVERT: B 82 ASP cc_start: 0.8105 (t70) cc_final: 0.7607 (t0) REVERT: B 86 TYR cc_start: 0.8838 (m-80) cc_final: 0.8345 (m-80) REVERT: B 139 ARG cc_start: 0.8335 (mtm110) cc_final: 0.7640 (mtp85) REVERT: B 163 GLU cc_start: 0.7422 (pt0) cc_final: 0.7064 (pm20) REVERT: B 192 LYS cc_start: 0.8235 (tttt) cc_final: 0.7934 (ttmm) REVERT: B 294 ASP cc_start: 0.8195 (t0) cc_final: 0.7644 (p0) REVERT: B 308 LYS cc_start: 0.8060 (mttp) cc_final: 0.7611 (tmtt) REVERT: B 319 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8148 (m) REVERT: B 334 ASP cc_start: 0.7533 (p0) cc_final: 0.6819 (p0) REVERT: B 403 HIS cc_start: 0.8313 (p90) cc_final: 0.8040 (p90) REVERT: B 425 ILE cc_start: 0.8514 (pt) cc_final: 0.8310 (mt) outliers start: 27 outliers final: 20 residues processed: 225 average time/residue: 0.1820 time to fit residues: 56.0238 Evaluate side-chains 212 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 149 GLU 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 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 76 LEU 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 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 46 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7764 Z= 0.243 Angle : 0.590 10.265 10532 Z= 0.302 Chirality : 0.046 0.239 1174 Planarity : 0.004 0.041 1336 Dihedral : 5.617 38.094 1146 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.51 % Allowed : 25.94 % Favored : 70.55 % 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: 0.51 (0.27), residues: 966 helix: 2.48 (0.31), residues: 282 sheet: -0.19 (0.32), residues: 258 loop : -0.78 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 88 HIS 0.003 0.001 HIS B 108 PHE 0.026 0.002 PHE B 208 TYR 0.019 0.001 TYR A 284 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 214 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 CYS cc_start: 0.6411 (m) cc_final: 0.6058 (m) REVERT: A 76 LEU cc_start: 0.9201 (mp) cc_final: 0.8850 (mm) REVERT: A 139 ARG cc_start: 0.8019 (mtm110) cc_final: 0.7737 (mtp85) REVERT: A 163 GLU cc_start: 0.7580 (pt0) cc_final: 0.7198 (pm20) REVERT: A 294 ASP cc_start: 0.8194 (t0) cc_final: 0.7535 (p0) REVERT: A 308 LYS cc_start: 0.8126 (mttp) cc_final: 0.7616 (tmtt) REVERT: A 319 THR cc_start: 0.8598 (OUTLIER) cc_final: 0.8188 (m) REVERT: A 334 ASP cc_start: 0.7759 (p0) cc_final: 0.7126 (p0) REVERT: A 358 TYR cc_start: 0.7062 (m-80) cc_final: 0.6598 (m-80) REVERT: A 479 PHE cc_start: 0.8555 (m-80) cc_final: 0.8293 (m-80) REVERT: B 86 TYR cc_start: 0.8819 (m-80) cc_final: 0.8440 (m-80) REVERT: B 139 ARG cc_start: 0.8119 (mtm110) cc_final: 0.7688 (mtp85) REVERT: B 163 GLU cc_start: 0.7539 (pt0) cc_final: 0.7221 (pm20) REVERT: B 294 ASP cc_start: 0.8246 (t0) cc_final: 0.7682 (p0) REVERT: B 308 LYS cc_start: 0.8084 (mttp) cc_final: 0.7620 (tttm) REVERT: B 319 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8229 (m) REVERT: B 334 ASP cc_start: 0.7689 (p0) cc_final: 0.7102 (p0) REVERT: B 425 ILE cc_start: 0.8560 (pt) cc_final: 0.8345 (mt) outliers start: 28 outliers final: 22 residues processed: 206 average time/residue: 0.1775 time to fit residues: 50.0319 Evaluate side-chains 205 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 181 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 201 VAL Chi-restraints excluded: chain A residue 241 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 426 ILE Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 475 CYS Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 484 VAL 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 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 426 ILE Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 475 CYS Chi-restraints excluded: chain B residue 481 THR 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: 0.9980 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 31 optimal weight: 9.9990 chunk 78 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.3560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.137362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.119559 restraints weight = 9099.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.119834 restraints weight = 8636.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.120383 restraints weight = 7867.602| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7764 Z= 0.199 Angle : 0.559 9.303 10532 Z= 0.287 Chirality : 0.045 0.242 1174 Planarity : 0.004 0.038 1336 Dihedral : 5.548 37.325 1146 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.63 % Allowed : 25.94 % Favored : 70.43 % 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: 0.59 (0.27), residues: 966 helix: 2.51 (0.31), residues: 282 sheet: -0.12 (0.33), residues: 244 loop : -0.70 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 88 HIS 0.005 0.001 HIS B 138 PHE 0.028 0.002 PHE B 208 TYR 0.013 0.001 TYR B 13 ARG 0.008 0.000 ARG B 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1795.53 seconds wall clock time: 32 minutes 45.22 seconds (1965.22 seconds total)