Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 08:26:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/08_2023/7x1r_32947_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/08_2023/7x1r_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_32947/08_2023/7x1r_32947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/08_2023/7x1r_32947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/08_2023/7x1r_32947_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x1r_32947/08_2023/7x1r_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 4.43, per 1000 atoms: 0.58 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: 2.99 Conformation dependent library (CDL) restraints added in 1.0 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: 1.41 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: 2.09 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: 4181 17.52 - 35.03: 311 35.03 - 52.55: 58 52.55 - 70.06: 14 70.06 - 87.58: 16 Dihedral angle restraints: 4580 sinusoidal: 1826 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 4577 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: 0.100 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: 0.990 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.490 Find NCS groups from input model: 0.390 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- 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 : 14.078 87.578 2830 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 % 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 *********************** 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 : 0.866 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 276 average time/residue: 0.2308 time to fit residues: 82.0416 Evaluate side-chains 177 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 175 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0684 time to fit residues: 1.4328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 A 450 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN ** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN B 450 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 7764 Z= 0.174 Angle : 0.525 6.729 10532 Z= 0.278 Chirality : 0.045 0.157 1174 Planarity : 0.004 0.050 1336 Dihedral : 4.528 27.769 1060 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.88 % 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 (0.26), residues: 966 helix: 1.90 (0.29), residues: 290 sheet: 0.24 (0.34), residues: 256 loop : -0.82 (0.27), residues: 420 *********************** 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: 15 poor density : 197 time to evaluate : 0.876 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 205 average time/residue: 0.1945 time to fit residues: 54.0361 Evaluate side-chains 176 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 0.873 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0811 time to fit residues: 1.9531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 72 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 7764 Z= 0.345 Angle : 0.613 5.692 10532 Z= 0.321 Chirality : 0.048 0.162 1174 Planarity : 0.004 0.037 1336 Dihedral : 4.513 20.288 1060 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 4.14 % 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: 0.39 (0.27), residues: 966 helix: 2.14 (0.31), residues: 278 sheet: -0.07 (0.33), residues: 260 loop : -0.77 (0.27), residues: 428 *********************** 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 199 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 0.906 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 186 average time/residue: 0.1985 time to fit residues: 49.6591 Evaluate side-chains 182 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 0.896 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.0733 time to fit residues: 4.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 45 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS B 243 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3358 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= 0.203 Angle : 0.515 6.095 10532 Z= 0.271 Chirality : 0.045 0.152 1174 Planarity : 0.003 0.030 1336 Dihedral : 4.131 17.671 1060 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.26 % 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 (0.27), residues: 966 helix: 2.12 (0.32), residues: 290 sheet: -0.10 (0.33), residues: 246 loop : -0.73 (0.27), residues: 430 *********************** 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 190 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 172 time to evaluate : 0.797 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 181 average time/residue: 0.1858 time to fit residues: 45.9281 Evaluate side-chains 169 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 0.851 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0726 time to fit residues: 2.3818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 79 optimal weight: 0.0010 chunk 64 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 47 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 3.7994 ------------------------------------------------------------------------------- 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** A 450 GLN ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8137 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 7764 Z= 0.401 Angle : 0.642 7.856 10532 Z= 0.329 Chirality : 0.047 0.146 1174 Planarity : 0.004 0.027 1336 Dihedral : 4.477 20.706 1060 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.88 % 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: 0.12 (0.27), residues: 966 helix: 1.99 (0.32), residues: 278 sheet: -0.45 (0.33), residues: 248 loop : -0.82 (0.27), residues: 440 *********************** 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 190 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 0.923 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 179 average time/residue: 0.1881 time to fit residues: 46.4256 Evaluate side-chains 173 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 0.880 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0722 time to fit residues: 2.4082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 7764 Z= 0.164 Angle : 0.500 7.457 10532 Z= 0.261 Chirality : 0.044 0.170 1174 Planarity : 0.003 0.030 1336 Dihedral : 4.043 18.621 1060 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 1.25 % 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: 0.34 (0.27), residues: 966 helix: 2.38 (0.32), residues: 276 sheet: -0.55 (0.33), residues: 250 loop : -0.66 (0.27), residues: 440 *********************** 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 195 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 185 time to evaluate : 0.916 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 189 average time/residue: 0.1822 time to fit residues: 47.8236 Evaluate side-chains 176 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 169 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0730 time to fit residues: 2.1231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 67 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 138 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4287 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 : 0.526 6.287 10532 Z= 0.274 Chirality : 0.044 0.150 1174 Planarity : 0.003 0.030 1336 Dihedral : 3.945 18.088 1060 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 2.26 % 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: 0.32 (0.27), residues: 966 helix: 2.21 (0.32), residues: 290 sheet: -0.55 (0.32), residues: 250 loop : -0.67 (0.29), residues: 426 *********************** 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 196 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 0.884 Fit side-chains outliers start: 18 outliers final: 9 residues processed: 187 average time/residue: 0.1815 time to fit residues: 47.3187 Evaluate side-chains 180 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 0.871 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0734 time to fit residues: 2.4299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 17 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** A 450 GLN ** B 85 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: 0.8103 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 7764 Z= 0.330 Angle : 0.607 8.145 10532 Z= 0.316 Chirality : 0.046 0.149 1174 Planarity : 0.004 0.032 1336 Dihedral : 4.234 20.426 1060 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 1.50 % 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: 0.15 (0.27), residues: 966 helix: 2.23 (0.32), residues: 278 sheet: -0.82 (0.33), residues: 238 loop : -0.70 (0.27), residues: 450 *********************** 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 193 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 10 residues processed: 185 average time/residue: 0.1886 time to fit residues: 47.6219 Evaluate side-chains 183 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 173 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0735 time to fit residues: 2.5606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.0030 chunk 88 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.0050 chunk 67 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 77 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 91 optimal weight: 0.0070 overall best weight: 0.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 7764 Z= 0.164 Angle : 0.531 8.768 10532 Z= 0.276 Chirality : 0.044 0.179 1174 Planarity : 0.003 0.031 1336 Dihedral : 3.868 17.353 1060 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer Outliers : 0.13 % 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 (0.28), residues: 966 helix: 2.30 (0.32), residues: 288 sheet: -0.67 (0.33), residues: 250 loop : -0.62 (0.29), residues: 428 *********************** 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 193 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.881 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 193 average time/residue: 0.2079 time to fit residues: 53.8036 Evaluate side-chains 172 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 171 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0737 time to fit residues: 1.3369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 7 optimal weight: 0.0670 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8118 ------------------------------------------------------------------------------- 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 85 ASN ** B 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4760 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= 0.191 Angle : 0.560 9.442 10532 Z= 0.290 Chirality : 0.045 0.211 1174 Planarity : 0.003 0.030 1336 Dihedral : 3.791 16.955 1060 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.63 % 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 (0.28), residues: 966 helix: 2.31 (0.32), residues: 288 sheet: -0.69 (0.32), residues: 250 loop : -0.61 (0.29), residues: 428 ********************** 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 178 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 0.999 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 175 average time/residue: 0.1906 time to fit residues: 46.1383 Evaluate side-chains 170 residues out of total 798 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 0.977 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0761 time to fit residues: 1.5363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** B 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.137851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.119063 restraints weight = 9059.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.121012 restraints weight = 6562.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.122556 restraints weight = 5197.190| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4765 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= 0.224 Angle : 0.570 9.233 10532 Z= 0.296 Chirality : 0.045 0.164 1174 Planarity : 0.004 0.036 1336 Dihedral : 3.881 17.711 1060 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.63 % 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: 0.48 (0.27), residues: 966 helix: 2.51 (0.32), residues: 278 sheet: -0.62 (0.34), residues: 214 loop : -0.52 (0.28), residues: 474 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.72 seconds wall clock time: 32 minutes 37.22 seconds (1957.22 seconds total)