Starting phenix.real_space_refine on Sat Jul 4 09:12:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i5n_35196/07_2026/8i5n_35196_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i5n_35196/07_2026/8i5n_35196.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i5n_35196/07_2026/8i5n_35196_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i5n_35196/07_2026/8i5n_35196_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i5n_35196/07_2026/8i5n_35196.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i5n_35196/07_2026/8i5n_35196.map" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.003 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 P 12 5.49 5 S 36 5.16 5 C 6484 2.51 5 N 1648 2.21 5 O 1840 1.98 5 H 10060 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20080 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "B" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "C" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "D" Number of atoms: 4983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 4983 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 11, 'TRANS': 298} Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 3.32, per 1000 atoms: 0.17 Number of scatterers: 20080 At special positions: 0 Unit cell: (96.33, 96.33, 113.568, 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) S 36 16.00 P 12 15.00 O 1840 8.00 N 1648 7.00 C 6484 6.00 H 10060 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 140 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 140 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 140 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 140 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 605.1 milliseconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 24 sheets defined 32.3% alpha, 29.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 46 through 54 removed outlier: 3.612A pdb=" N LEU A 50 " --> pdb=" O ASP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 61 Processing helix chain 'A' and resid 63 through 93 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 140 through 171 removed outlier: 3.619A pdb=" N ILE A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 177 removed outlier: 3.905A pdb=" N GLU A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.612A pdb=" N LEU B 50 " --> pdb=" O ASP B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 61 Processing helix chain 'B' and resid 63 through 93 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 140 through 171 removed outlier: 3.619A pdb=" N ILE B 144 " --> pdb=" O CYS B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 177 removed outlier: 3.903A pdb=" N GLU B 177 " --> pdb=" O LYS B 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.613A pdb=" N LEU C 50 " --> pdb=" O ASP C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 61 Processing helix chain 'C' and resid 63 through 93 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 140 through 171 removed outlier: 3.619A pdb=" N ILE C 144 " --> pdb=" O CYS C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.903A pdb=" N GLU C 177 " --> pdb=" O LYS C 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 54 removed outlier: 3.613A pdb=" N LEU D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 61 Processing helix chain 'D' and resid 63 through 93 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 140 through 171 removed outlier: 3.618A pdb=" N ILE D 144 " --> pdb=" O CYS D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 177 removed outlier: 3.904A pdb=" N GLU D 177 " --> pdb=" O LYS D 173 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 42 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA3, first strand: chain 'A' and resid 179 through 181 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 237 Processing sheet with id=AA5, first strand: chain 'A' and resid 233 through 237 removed outlier: 4.154A pdb=" N CYS A 211 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER A 284 " --> pdb=" O CYS A 211 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 213 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 282 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 215 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 280 " --> pdb=" O GLY A 215 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 217 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU A 278 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 311 Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 317 removed outlier: 5.927A pdb=" N TYR A 323 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N GLU B 42 " --> pdb=" O TYR A 323 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ALA A 325 " --> pdb=" O GLU B 42 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 233 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 233 through 237 removed outlier: 4.153A pdb=" N CYS B 211 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER B 284 " --> pdb=" O CYS B 211 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL B 213 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE B 282 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY B 215 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 280 " --> pdb=" O GLY B 215 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU B 217 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLU B 278 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 309 through 311 Processing sheet with id=AB4, first strand: chain 'B' and resid 315 through 317 Processing sheet with id=AB5, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AB7, first strand: chain 'C' and resid 233 through 237 Processing sheet with id=AB8, first strand: chain 'C' and resid 233 through 237 removed outlier: 4.154A pdb=" N CYS C 211 " --> pdb=" O SER C 284 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER C 284 " --> pdb=" O CYS C 211 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL C 213 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE C 282 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY C 215 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 280 " --> pdb=" O GLY C 215 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU C 217 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU C 278 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 309 through 311 Processing sheet with id=AC1, first strand: chain 'C' and resid 315 through 317 removed outlier: 6.105A pdb=" N TYR C 323 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N GLU D 42 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ALA C 325 " --> pdb=" O GLU D 42 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AC3, first strand: chain 'D' and resid 179 through 181 Processing sheet with id=AC4, first strand: chain 'D' and resid 233 through 237 Processing sheet with id=AC5, first strand: chain 'D' and resid 233 through 237 removed outlier: 4.154A pdb=" N CYS D 211 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N SER D 284 " --> pdb=" O CYS D 211 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D 213 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE D 282 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N GLY D 215 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 280 " --> pdb=" O GLY D 215 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 217 " --> pdb=" O GLU D 278 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLU D 278 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 309 through 311 458 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.79 - 1.00: 10045 1.00 - 1.20: 19 1.20 - 1.40: 4174 1.40 - 1.61: 6002 1.61 - 1.81: 68 Bond restraints: 20308 Sorted by residual: bond pdb=" O51 PIO D 401 " pdb=" P5 PIO D 401 " ideal model delta sigma weight residual 1.528 1.455 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" O51 PIO A 401 " pdb=" P5 PIO A 401 " ideal model delta sigma weight residual 1.528 1.455 0.073 2.00e-02 2.50e+03 1.31e+01 bond pdb=" O51 PIO C 401 " pdb=" P5 PIO C 401 " ideal model delta sigma weight residual 1.528 1.456 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O51 PIO B 401 " pdb=" P5 PIO B 401 " ideal model delta sigma weight residual 1.528 1.456 0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O43 PIO D 401 " pdb=" P4 PIO D 401 " ideal model delta sigma weight residual 1.529 1.458 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 20303 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.60: 36654 10.60 - 21.20: 24 21.20 - 31.80: 11 31.80 - 42.41: 21 42.41 - 53.01: 2 Bond angle restraints: 36712 Sorted by residual: angle pdb=" CA LYS A 322 " pdb=" CB LYS A 322 " pdb=" HB3 LYS A 322 " ideal model delta sigma weight residual 109.00 55.99 53.01 3.00e+00 1.11e-01 3.12e+02 angle pdb=" CG LYS A 322 " pdb=" CB LYS A 322 " pdb=" HB3 LYS A 322 " ideal model delta sigma weight residual 108.00 62.55 45.45 3.00e+00 1.11e-01 2.30e+02 angle pdb=" CG1 VAL C 334 " pdb=" CB VAL C 334 " pdb=" HB VAL C 334 " ideal model delta sigma weight residual 108.00 69.49 38.51 3.00e+00 1.11e-01 1.65e+02 angle pdb=" OG1 THR A 127 " pdb=" CB THR A 127 " pdb=" HB THR A 127 " ideal model delta sigma weight residual 109.00 70.91 38.09 3.00e+00 1.11e-01 1.61e+02 angle pdb=" HZ1 LYS A 322 " pdb=" NZ LYS A 322 " pdb=" HZ3 LYS A 322 " ideal model delta sigma weight residual 109.00 72.83 36.17 3.00e+00 1.11e-01 1.45e+02 ... (remaining 36707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 8545 17.38 - 34.76: 660 34.76 - 52.15: 199 52.15 - 69.53: 69 69.53 - 86.91: 7 Dihedral angle restraints: 9480 sinusoidal: 5112 harmonic: 4368 Sorted by residual: dihedral pdb=" CA ASN A 104 " pdb=" C ASN A 104 " pdb=" N HIS A 105 " pdb=" CA HIS A 105 " ideal model delta harmonic sigma weight residual 180.00 -152.96 -27.04 0 5.00e+00 4.00e-02 2.93e+01 dihedral pdb=" CA ASN B 104 " pdb=" C ASN B 104 " pdb=" N HIS B 105 " pdb=" CA HIS B 105 " ideal model delta harmonic sigma weight residual -180.00 -152.98 -27.02 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ASN C 104 " pdb=" C ASN C 104 " pdb=" N HIS C 105 " pdb=" CA HIS C 105 " ideal model delta harmonic sigma weight residual 180.00 -152.99 -27.01 0 5.00e+00 4.00e-02 2.92e+01 ... (remaining 9477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 1620 0.173 - 0.345: 24 0.345 - 0.518: 0 0.518 - 0.691: 4 0.691 - 0.863: 4 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CB VAL B 145 " pdb=" CA VAL B 145 " pdb=" CG1 VAL B 145 " pdb=" CG2 VAL B 145 " both_signs ideal model delta sigma weight residual False -2.63 -1.77 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" CB VAL D 145 " pdb=" CA VAL D 145 " pdb=" CG1 VAL D 145 " pdb=" CG2 VAL D 145 " both_signs ideal model delta sigma weight residual False -2.63 -1.77 -0.86 2.00e-01 2.50e+01 1.86e+01 chirality pdb=" CB VAL C 145 " pdb=" CA VAL C 145 " pdb=" CG1 VAL C 145 " pdb=" CG2 VAL C 145 " both_signs ideal model delta sigma weight residual False -2.63 -1.77 -0.86 2.00e-01 2.50e+01 1.85e+01 ... (remaining 1649 not shown) Planarity restraints: 2900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 295 " 0.019 2.00e-02 2.50e+03 1.69e-02 4.26e+00 pdb=" CD GLN D 295 " -0.027 2.00e-02 2.50e+03 pdb=" OE1 GLN D 295 " 0.001 2.00e-02 2.50e+03 pdb=" NE2 GLN D 295 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN D 295 " 0.021 2.00e-02 2.50e+03 pdb="HE22 GLN D 295 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 295 " -0.008 2.00e-02 2.50e+03 1.55e-02 3.61e+00 pdb=" CD GLN B 295 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 295 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN B 295 " 0.012 2.00e-02 2.50e+03 pdb="HE21 GLN B 295 " -0.011 2.00e-02 2.50e+03 pdb="HE22 GLN B 295 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 295 " -0.009 2.00e-02 2.50e+03 1.50e-02 3.36e+00 pdb=" CD GLN C 295 " 0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN C 295 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN C 295 " 0.011 2.00e-02 2.50e+03 pdb="HE21 GLN C 295 " -0.009 2.00e-02 2.50e+03 pdb="HE22 GLN C 295 " -0.008 2.00e-02 2.50e+03 ... (remaining 2897 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 796 2.10 - 2.73: 36895 2.73 - 3.35: 55945 3.35 - 3.98: 71807 3.98 - 4.60: 113591 Nonbonded interactions: 279034 Sorted by model distance: nonbonded pdb=" O LYS D 33 " pdb=" HG1 THR D 298 " model vdw 1.480 2.450 nonbonded pdb=" O LYS C 33 " pdb=" HG1 THR C 298 " model vdw 1.520 2.450 nonbonded pdb=" O MET D 62 " pdb=" HZ3 LYS D 168 " model vdw 1.537 2.450 nonbonded pdb=" O MET B 62 " pdb=" HZ3 LYS B 168 " model vdw 1.540 2.450 nonbonded pdb=" O MET C 62 " pdb=" HZ3 LYS C 168 " model vdw 1.543 2.450 ... (remaining 279029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 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: 0.110 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 16.950 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:6.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 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 : 0.012 0.075 10252 Z= 0.531 Angle : 1.279 19.786 13960 Z= 0.620 Chirality : 0.081 0.863 1652 Planarity : 0.005 0.044 1708 Dihedral : 13.568 71.799 3644 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.47 % Favored : 92.21 % Rotamer: Outliers : 1.47 % Allowed : 4.41 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.20), residues: 1232 helix: -2.60 (0.19), residues: 372 sheet: -1.13 (0.37), residues: 196 loop : -1.83 (0.21), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 28 TYR 0.012 0.002 TYR B 300 PHE 0.026 0.003 PHE D 71 TRP 0.004 0.001 TRP C 56 HIS 0.004 0.002 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01224 / 0.53 (10248) covalent geometry : angle 1.27912 / 0.62 (13952) SS BOND : bond 0.00140 / 0.07 ( 4) SS BOND : angle 1.50151 / 0.92 ( 8) hydrogen bonds : bond 0.11598 / 7.18 ( 434) hydrogen bonds : angle 7.25067 / 5.22 ( 1338) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 275 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.7006 (mmm) cc_final: 0.6130 (mtp) REVERT: A 277 PHE cc_start: 0.5834 (p90) cc_final: 0.5587 (p90) REVERT: A 324 VAL cc_start: 0.8116 (t) cc_final: 0.7785 (p) REVERT: B 190 HIS cc_start: 0.7071 (t70) cc_final: 0.6700 (t-90) REVERT: B 203 MET cc_start: 0.6310 (mmm) cc_final: 0.6086 (mtt) REVERT: C 30 VAL cc_start: 0.7949 (t) cc_final: 0.7405 (t) REVERT: C 203 MET cc_start: 0.6743 (mmm) cc_final: 0.6275 (mtt) REVERT: D 30 VAL cc_start: 0.7875 (t) cc_final: 0.7263 (t) REVERT: D 203 MET cc_start: 0.6843 (mmm) cc_final: 0.6440 (mtt) outliers start: 16 outliers final: 6 residues processed: 287 average time/residue: 0.7229 time to fit residues: 230.9862 Evaluate side-chains 167 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain D residue 54 ASP Chi-restraints excluded: chain D residue 291 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 219 GLN A 228 ASN A 232 ASN ** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 ASN B 232 ASN C 183 GLN C 190 HIS C 191 ASN C 219 GLN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5463 r_free = 0.5463 target = 0.248931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.216921 restraints weight = 46683.689| |-----------------------------------------------------------------------------| r_work (start): 0.5122 rms_B_bonded: 3.87 r_work: 0.4992 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.4992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10252 Z= 0.150 Angle : 0.734 15.406 13960 Z= 0.378 Chirality : 0.117 1.595 1652 Planarity : 0.005 0.052 1708 Dihedral : 7.602 59.345 1376 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.30 % Allowed : 13.60 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.22), residues: 1232 helix: -0.32 (0.24), residues: 372 sheet: -0.75 (0.36), residues: 200 loop : -1.27 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 36 TYR 0.009 0.001 TYR D 300 PHE 0.028 0.002 PHE A 165 TRP 0.011 0.001 TRP B 56 HIS 0.008 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (10248) covalent geometry : angle 0.73287 / 0.38 (13952) SS BOND : bond 0.00083 / 0.04 ( 4) SS BOND : angle 1.62699 / 1.03 ( 8) hydrogen bonds : bond 0.05740 / 3.82 ( 434) hydrogen bonds : angle 5.57330 / 3.96 ( 1338) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7704 (mp0) REVERT: A 46 ASP cc_start: 0.6587 (t0) cc_final: 0.6357 (t0) REVERT: A 190 HIS cc_start: 0.7738 (OUTLIER) cc_final: 0.7452 (t-90) REVERT: A 203 MET cc_start: 0.7012 (mmm) cc_final: 0.6409 (mtt) REVERT: A 327 PHE cc_start: 0.7667 (m-80) cc_final: 0.7451 (m-10) REVERT: B 40 ARG cc_start: 0.7445 (mmp-170) cc_final: 0.7176 (mmp80) REVERT: B 190 HIS cc_start: 0.7131 (t70) cc_final: 0.6858 (t70) REVERT: B 203 MET cc_start: 0.6235 (mmm) cc_final: 0.5885 (mtt) REVERT: B 265 LEU cc_start: 0.8896 (mp) cc_final: 0.8664 (mm) REVERT: C 203 MET cc_start: 0.6802 (mmm) cc_final: 0.6584 (mtt) REVERT: C 265 LEU cc_start: 0.9141 (mt) cc_final: 0.8920 (mm) REVERT: C 295 GLN cc_start: 0.7948 (tt0) cc_final: 0.7347 (mm-40) REVERT: D 190 HIS cc_start: 0.7177 (OUTLIER) cc_final: 0.6878 (t-90) REVERT: D 203 MET cc_start: 0.6901 (mmm) cc_final: 0.6479 (mtt) REVERT: D 261 GLU cc_start: 0.7175 (tp30) cc_final: 0.6898 (mp0) outliers start: 25 outliers final: 10 residues processed: 223 average time/residue: 0.6180 time to fit residues: 156.1267 Evaluate side-chains 178 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 166 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 190 HIS Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 190 HIS Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 0.0000 chunk 94 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN A 219 GLN A 235 ASN B 183 GLN C 228 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5381 r_free = 0.5381 target = 0.241670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5070 r_free = 0.5070 target = 0.209348 restraints weight = 46467.795| |-----------------------------------------------------------------------------| r_work (start): 0.5010 rms_B_bonded: 3.86 r_work: 0.4872 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.4872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10252 Z= 0.199 Angle : 0.725 15.532 13960 Z= 0.380 Chirality : 0.120 1.639 1652 Planarity : 0.004 0.052 1708 Dihedral : 6.936 51.612 1370 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.76 % Allowed : 17.56 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.22), residues: 1232 helix: 0.27 (0.24), residues: 372 sheet: -1.05 (0.34), residues: 216 loop : -0.82 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.015 0.002 TYR D 189 PHE 0.032 0.002 PHE A 165 TRP 0.004 0.001 TRP A 56 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (10248) covalent geometry : angle 0.72336 / 0.38 (13952) SS BOND : bond 0.00249 / 0.13 ( 4) SS BOND : angle 2.18826 / 1.43 ( 8) hydrogen bonds : bond 0.05869 / 3.92 ( 434) hydrogen bonds : angle 5.31084 / 3.79 ( 1338) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7630 (mp0) REVERT: A 46 ASP cc_start: 0.6627 (t0) cc_final: 0.6188 (t0) REVERT: A 203 MET cc_start: 0.6534 (mmm) cc_final: 0.6218 (mtp) REVERT: A 327 PHE cc_start: 0.7685 (m-80) cc_final: 0.7313 (m-80) REVERT: B 28 ARG cc_start: 0.7852 (ptm160) cc_final: 0.7164 (ptm-80) REVERT: B 46 ASP cc_start: 0.6582 (t0) cc_final: 0.6329 (t0) REVERT: B 203 MET cc_start: 0.6468 (mmm) cc_final: 0.6150 (mtt) REVERT: B 265 LEU cc_start: 0.9077 (mp) cc_final: 0.8850 (mm) REVERT: B 278 GLU cc_start: 0.5736 (mt-10) cc_final: 0.4398 (mp0) REVERT: B 295 GLN cc_start: 0.7756 (tt0) cc_final: 0.7332 (mm-40) REVERT: C 203 MET cc_start: 0.7100 (mmm) cc_final: 0.6217 (mtt) REVERT: D 203 MET cc_start: 0.7084 (mmm) cc_final: 0.6201 (mtt) outliers start: 30 outliers final: 16 residues processed: 211 average time/residue: 0.5182 time to fit residues: 127.1922 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 104 ASN Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 121 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 HIS D 228 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5360 r_free = 0.5360 target = 0.238563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5046 r_free = 0.5046 target = 0.206056 restraints weight = 47045.645| |-----------------------------------------------------------------------------| r_work (start): 0.4994 rms_B_bonded: 3.90 r_work: 0.4866 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.4866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10252 Z= 0.179 Angle : 0.707 15.552 13960 Z= 0.366 Chirality : 0.122 1.664 1652 Planarity : 0.004 0.053 1708 Dihedral : 6.732 52.572 1370 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.11 % Allowed : 19.76 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.21), residues: 1232 helix: 0.35 (0.24), residues: 396 sheet: -1.12 (0.34), residues: 216 loop : -1.06 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.009 0.001 TYR A 323 PHE 0.033 0.002 PHE A 165 TRP 0.003 0.001 TRP A 56 HIS 0.007 0.001 HIS B 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (10248) covalent geometry : angle 0.70557 / 0.37 (13952) SS BOND : bond 0.00273 / 0.14 ( 4) SS BOND : angle 2.00625 / 1.27 ( 8) hydrogen bonds : bond 0.05675 / 3.77 ( 434) hydrogen bonds : angle 5.22469 / 3.74 ( 1338) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6538 (t0) cc_final: 0.6268 (t70) REVERT: A 267 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: A 327 PHE cc_start: 0.7654 (m-80) cc_final: 0.7330 (t80) REVERT: B 28 ARG cc_start: 0.7855 (ptm160) cc_final: 0.7497 (ppt170) REVERT: B 40 ARG cc_start: 0.7553 (mmp80) cc_final: 0.7319 (mmp80) REVERT: B 46 ASP cc_start: 0.6506 (t0) cc_final: 0.6130 (t0) REVERT: B 203 MET cc_start: 0.6511 (mmm) cc_final: 0.6130 (mtt) REVERT: B 265 LEU cc_start: 0.9145 (mp) cc_final: 0.8938 (mm) REVERT: B 278 GLU cc_start: 0.5699 (mt-10) cc_final: 0.4409 (mp0) REVERT: B 295 GLN cc_start: 0.7780 (tt0) cc_final: 0.7326 (mt0) REVERT: C 203 MET cc_start: 0.7217 (mmm) cc_final: 0.6386 (mtt) REVERT: C 305 ILE cc_start: 0.8806 (tp) cc_final: 0.8299 (mp) REVERT: D 75 PHE cc_start: 0.6631 (m-80) cc_final: 0.6350 (m-80) REVERT: D 104 ASN cc_start: 0.8456 (m-40) cc_final: 0.8220 (p0) REVERT: D 203 MET cc_start: 0.7167 (mmm) cc_final: 0.6583 (mtt) REVERT: D 305 ILE cc_start: 0.8878 (tp) cc_final: 0.8402 (mp) outliers start: 23 outliers final: 17 residues processed: 184 average time/residue: 0.5449 time to fit residues: 116.3359 Evaluate side-chains 177 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 205 LYS Chi-restraints excluded: chain A residue 267 ASP Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 205 LYS Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 260 ASP Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 22 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 119 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5371 r_free = 0.5371 target = 0.239392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.207278 restraints weight = 47367.187| |-----------------------------------------------------------------------------| r_work (start): 0.5057 rms_B_bonded: 3.89 r_work: 0.4981 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10252 Z= 0.143 Angle : 0.667 15.518 13960 Z= 0.344 Chirality : 0.122 1.660 1652 Planarity : 0.003 0.046 1708 Dihedral : 6.368 53.026 1370 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.84 % Allowed : 20.04 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.22), residues: 1232 helix: 0.75 (0.24), residues: 396 sheet: -0.95 (0.35), residues: 216 loop : -0.96 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 175 TYR 0.007 0.001 TYR C 51 PHE 0.035 0.002 PHE C 165 TRP 0.003 0.001 TRP B 56 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (10248) covalent geometry : angle 0.66554 / 0.34 (13952) SS BOND : bond 0.00154 / 0.08 ( 4) SS BOND : angle 1.78508 / 1.11 ( 8) hydrogen bonds : bond 0.05364 / 3.54 ( 434) hydrogen bonds : angle 5.09948 / 3.65 ( 1338) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6470 (t0) cc_final: 0.6153 (t70) REVERT: A 295 GLN cc_start: 0.7824 (mt0) cc_final: 0.7035 (mm-40) REVERT: B 28 ARG cc_start: 0.7994 (ptm160) cc_final: 0.7619 (ppt170) REVERT: B 40 ARG cc_start: 0.7405 (mmp80) cc_final: 0.7180 (mmp80) REVERT: B 46 ASP cc_start: 0.6385 (t0) cc_final: 0.5983 (t0) REVERT: B 203 MET cc_start: 0.6556 (mmm) cc_final: 0.6114 (mtt) REVERT: B 278 GLU cc_start: 0.5606 (mt-10) cc_final: 0.4196 (mp0) REVERT: B 295 GLN cc_start: 0.7798 (tt0) cc_final: 0.7333 (mt0) REVERT: C 203 MET cc_start: 0.7140 (mmm) cc_final: 0.6484 (mtt) REVERT: C 305 ILE cc_start: 0.8853 (tp) cc_final: 0.8353 (mp) REVERT: D 104 ASN cc_start: 0.8500 (m-40) cc_final: 0.8197 (p0) REVERT: D 203 MET cc_start: 0.7046 (mmm) cc_final: 0.6566 (mtt) REVERT: D 265 LEU cc_start: 0.8501 (mm) cc_final: 0.8155 (tt) REVERT: D 305 ILE cc_start: 0.8840 (tp) cc_final: 0.8435 (mp) outliers start: 20 outliers final: 13 residues processed: 189 average time/residue: 0.5071 time to fit residues: 111.5286 Evaluate side-chains 169 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 156 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 291 SER Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.0770 chunk 32 optimal weight: 10.0000 chunk 116 optimal weight: 0.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5337 r_free = 0.5337 target = 0.235753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5026 r_free = 0.5026 target = 0.203226 restraints weight = 47356.342| |-----------------------------------------------------------------------------| r_work (start): 0.5022 rms_B_bonded: 3.86 r_work: 0.4951 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.5487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 10252 Z= 0.172 Angle : 0.689 15.467 13960 Z= 0.358 Chirality : 0.123 1.698 1652 Planarity : 0.004 0.048 1708 Dihedral : 6.343 52.354 1370 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.02 % Allowed : 22.15 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.22), residues: 1232 helix: 0.72 (0.24), residues: 396 sheet: -0.96 (0.35), residues: 216 loop : -0.84 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 175 TYR 0.009 0.001 TYR A 323 PHE 0.035 0.002 PHE D 165 TRP 0.004 0.001 TRP A 56 HIS 0.004 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (10248) covalent geometry : angle 0.68751 / 0.36 (13952) SS BOND : bond 0.00254 / 0.13 ( 4) SS BOND : angle 1.83325 / 1.12 ( 8) hydrogen bonds : bond 0.05536 / 3.64 ( 434) hydrogen bonds : angle 5.14881 / 3.69 ( 1338) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6532 (t0) cc_final: 0.6215 (t70) REVERT: A 295 GLN cc_start: 0.7821 (mt0) cc_final: 0.7037 (mm-40) REVERT: B 40 ARG cc_start: 0.7434 (mmp80) cc_final: 0.7208 (mmp80) REVERT: B 46 ASP cc_start: 0.6516 (t0) cc_final: 0.6203 (t70) REVERT: B 203 MET cc_start: 0.6547 (mmm) cc_final: 0.6096 (mtt) REVERT: B 295 GLN cc_start: 0.7797 (tt0) cc_final: 0.7226 (mt0) REVERT: C 104 ASN cc_start: 0.8680 (m-40) cc_final: 0.8236 (p0) REVERT: C 203 MET cc_start: 0.7058 (mmm) cc_final: 0.6506 (mtt) REVERT: C 267 ASP cc_start: 0.8217 (m-30) cc_final: 0.7913 (t0) REVERT: C 305 ILE cc_start: 0.8844 (tp) cc_final: 0.8314 (mp) REVERT: D 104 ASN cc_start: 0.8546 (m-40) cc_final: 0.8229 (OUTLIER) REVERT: D 203 MET cc_start: 0.7129 (mmm) cc_final: 0.6853 (mtt) REVERT: D 265 LEU cc_start: 0.8502 (mm) cc_final: 0.7887 (tt) REVERT: D 305 ILE cc_start: 0.8943 (tp) cc_final: 0.8512 (mp) outliers start: 22 outliers final: 14 residues processed: 183 average time/residue: 0.4914 time to fit residues: 105.9872 Evaluate side-chains 164 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.230643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.197995 restraints weight = 48334.031| |-----------------------------------------------------------------------------| r_work (start): 0.4930 rms_B_bonded: 3.87 r_work: 0.4806 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.4806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10252 Z= 0.227 Angle : 0.739 15.445 13960 Z= 0.388 Chirality : 0.123 1.709 1652 Planarity : 0.004 0.055 1708 Dihedral : 6.552 52.342 1369 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.76 % Allowed : 20.96 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1232 helix: 0.35 (0.24), residues: 396 sheet: -1.28 (0.34), residues: 216 loop : -0.73 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 28 TYR 0.010 0.002 TYR A 323 PHE 0.040 0.003 PHE D 165 TRP 0.006 0.001 TRP A 56 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.23 (10248) covalent geometry : angle 0.73755 / 0.39 (13952) SS BOND : bond 0.00421 / 0.21 ( 4) SS BOND : angle 2.29532 / 1.41 ( 8) hydrogen bonds : bond 0.05937 / 3.90 ( 434) hydrogen bonds : angle 5.36170 / 3.86 ( 1338) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6575 (t0) cc_final: 0.6334 (t70) REVERT: B 46 ASP cc_start: 0.6475 (t0) cc_final: 0.6187 (t70) REVERT: C 104 ASN cc_start: 0.8645 (m-40) cc_final: 0.8222 (p0) REVERT: C 203 MET cc_start: 0.7109 (mmm) cc_final: 0.6613 (mtt) REVERT: D 104 ASN cc_start: 0.8548 (m-40) cc_final: 0.8309 (p0) REVERT: D 203 MET cc_start: 0.6991 (mmm) cc_final: 0.6788 (mtt) REVERT: D 305 ILE cc_start: 0.8899 (tp) cc_final: 0.8398 (mp) outliers start: 30 outliers final: 22 residues processed: 184 average time/residue: 0.5037 time to fit residues: 108.5528 Evaluate side-chains 173 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.232463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.200212 restraints weight = 47568.991| |-----------------------------------------------------------------------------| r_work (start): 0.4934 rms_B_bonded: 3.84 r_work: 0.4810 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 10252 Z= 0.199 Angle : 0.719 15.447 13960 Z= 0.376 Chirality : 0.123 1.709 1652 Planarity : 0.004 0.053 1708 Dihedral : 6.463 52.510 1369 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.76 % Allowed : 21.60 % Favored : 75.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1232 helix: 0.40 (0.24), residues: 396 sheet: -1.39 (0.34), residues: 216 loop : -0.61 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 40 TYR 0.013 0.002 TYR B 300 PHE 0.042 0.003 PHE D 165 TRP 0.006 0.001 TRP D 56 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.20 (10248) covalent geometry : angle 0.71827 / 0.38 (13952) SS BOND : bond 0.00264 / 0.13 ( 4) SS BOND : angle 1.83559 / 1.12 ( 8) hydrogen bonds : bond 0.05741 / 3.75 ( 434) hydrogen bonds : angle 5.34032 / 3.84 ( 1338) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6549 (t0) cc_final: 0.6304 (t70) REVERT: A 267 ASP cc_start: 0.8668 (p0) cc_final: 0.8367 (m-30) REVERT: B 46 ASP cc_start: 0.6430 (t0) cc_final: 0.6156 (t70) REVERT: B 104 ASN cc_start: 0.8512 (m-40) cc_final: 0.8048 (p0) REVERT: C 203 MET cc_start: 0.7025 (mmm) cc_final: 0.6546 (mtt) REVERT: D 104 ASN cc_start: 0.8572 (m-40) cc_final: 0.8311 (p0) REVERT: D 295 GLN cc_start: 0.8001 (mt0) cc_final: 0.7760 (mt0) outliers start: 30 outliers final: 21 residues processed: 178 average time/residue: 0.4545 time to fit residues: 95.5160 Evaluate side-chains 170 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 149 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 291 SER Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 322 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 86 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.232368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4977 r_free = 0.4977 target = 0.199929 restraints weight = 47640.213| |-----------------------------------------------------------------------------| r_work (start): 0.4932 rms_B_bonded: 3.84 r_work: 0.4807 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.4807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10252 Z= 0.161 Angle : 0.692 15.451 13960 Z= 0.359 Chirality : 0.123 1.722 1652 Planarity : 0.003 0.045 1708 Dihedral : 6.283 52.444 1369 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.57 % Allowed : 22.15 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1232 helix: 0.58 (0.24), residues: 396 sheet: -1.43 (0.34), residues: 216 loop : -0.55 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 40 TYR 0.009 0.001 TYR A 309 PHE 0.017 0.002 PHE B 71 TRP 0.005 0.001 TRP C 307 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (10248) covalent geometry : angle 0.69145 / 0.36 (13952) SS BOND : bond 0.00205 / 0.10 ( 4) SS BOND : angle 1.62995 / 0.98 ( 8) hydrogen bonds : bond 0.05495 / 3.58 ( 434) hydrogen bonds : angle 5.24935 / 3.78 ( 1338) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 160 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6553 (t0) cc_final: 0.6323 (t70) REVERT: A 267 ASP cc_start: 0.8686 (p0) cc_final: 0.8340 (m-30) REVERT: B 104 ASN cc_start: 0.8506 (m-40) cc_final: 0.8077 (p0) REVERT: C 173 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.6697 (mttp) REVERT: C 203 MET cc_start: 0.6913 (mmm) cc_final: 0.6634 (mtt) REVERT: C 295 GLN cc_start: 0.7850 (mt0) cc_final: 0.7590 (mt0) REVERT: D 104 ASN cc_start: 0.8551 (m-40) cc_final: 0.8301 (p0) REVERT: D 220 THR cc_start: 0.6593 (OUTLIER) cc_final: 0.6136 (m) REVERT: D 295 GLN cc_start: 0.8029 (mt0) cc_final: 0.7801 (mt0) outliers start: 28 outliers final: 18 residues processed: 175 average time/residue: 0.5244 time to fit residues: 106.4263 Evaluate side-chains 167 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5296 r_free = 0.5296 target = 0.231770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.199322 restraints weight = 47894.227| |-----------------------------------------------------------------------------| r_work (start): 0.4931 rms_B_bonded: 3.85 r_work: 0.4805 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6882 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10252 Z= 0.178 Angle : 0.704 15.476 13960 Z= 0.365 Chirality : 0.123 1.709 1652 Planarity : 0.004 0.064 1708 Dihedral : 6.247 52.130 1368 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.93 % Allowed : 23.35 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.23), residues: 1232 helix: 0.56 (0.24), residues: 396 sheet: -1.48 (0.33), residues: 216 loop : -0.50 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 40 TYR 0.010 0.001 TYR A 309 PHE 0.035 0.003 PHE A 165 TRP 0.005 0.001 TRP D 56 HIS 0.005 0.001 HIS D 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (10248) covalent geometry : angle 0.70274 / 0.36 (13952) SS BOND : bond 0.00272 / 0.14 ( 4) SS BOND : angle 1.68661 / 1.01 ( 8) hydrogen bonds : bond 0.05582 / 3.61 ( 434) hydrogen bonds : angle 5.28172 / 3.81 ( 1338) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 ASP cc_start: 0.6582 (t0) cc_final: 0.6343 (t70) REVERT: B 46 ASP cc_start: 0.6384 (t0) cc_final: 0.6157 (t70) REVERT: B 104 ASN cc_start: 0.8493 (m-40) cc_final: 0.8091 (p0) REVERT: C 173 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6679 (mttp) REVERT: C 203 MET cc_start: 0.6915 (mmm) cc_final: 0.6639 (mtt) REVERT: C 220 THR cc_start: 0.6749 (OUTLIER) cc_final: 0.6335 (m) REVERT: C 295 GLN cc_start: 0.8028 (mt0) cc_final: 0.7711 (mt0) REVERT: D 104 ASN cc_start: 0.8550 (m-40) cc_final: 0.8299 (p0) REVERT: D 220 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6117 (m) REVERT: D 295 GLN cc_start: 0.8038 (mt0) cc_final: 0.7756 (mt0) outliers start: 21 outliers final: 14 residues processed: 171 average time/residue: 0.5409 time to fit residues: 108.0335 Evaluate side-chains 170 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 291 SER Chi-restraints excluded: chain C residue 296 VAL Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain D residue 187 VAL Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 296 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 9.9990 chunk 67 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5258 r_free = 0.5258 target = 0.227998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.195439 restraints weight = 48494.432| |-----------------------------------------------------------------------------| r_work (start): 0.4877 rms_B_bonded: 3.87 r_work: 0.4751 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 10252 Z= 0.266 Angle : 0.781 15.426 13960 Z= 0.413 Chirality : 0.123 1.707 1652 Planarity : 0.004 0.060 1708 Dihedral : 6.668 51.227 1368 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.11 % Allowed : 23.53 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.22), residues: 1232 helix: 0.06 (0.23), residues: 396 sheet: -1.60 (0.33), residues: 216 loop : -0.62 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 175 TYR 0.012 0.002 TYR A 309 PHE 0.039 0.004 PHE A 165 TRP 0.010 0.002 TRP D 56 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (10248) covalent geometry : angle 0.78000 / 0.41 (13952) SS BOND : bond 0.00450 / 0.23 ( 4) SS BOND : angle 2.04460 / 1.25 ( 8) hydrogen bonds : bond 0.06175 / 4.02 ( 434) hydrogen bonds : angle 5.54960 / 4.01 ( 1338) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5161.47 seconds wall clock time: 88 minutes 12.31 seconds (5292.31 seconds total)