Starting phenix.real_space_refine on Wed Feb 4 01:08:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ip5_60759/02_2026/9ip5_60759.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ip5_60759/02_2026/9ip5_60759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ip5_60759/02_2026/9ip5_60759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ip5_60759/02_2026/9ip5_60759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ip5_60759/02_2026/9ip5_60759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ip5_60759/02_2026/9ip5_60759.map" } resolution = 3.52 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= 0.006 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 5466 2.51 5 N 1272 2.21 5 O 1374 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "D" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "E" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'C14': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'C14': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'C14': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'C14': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'C14': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {'C14': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 2.18, per 1000 atoms: 0.27 Number of scatterers: 8190 At special positions: 0 Unit cell: (94.905, 100.035, 82.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 78 16.00 O 1374 8.00 N 1272 7.00 C 5466 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " 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: 0.86 Conformation dependent library (CDL) restraints added in 347.7 milliseconds 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1872 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 78.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 21 through 46 removed outlier: 3.913A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLU A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N THR A 44 " --> pdb=" O ILE A 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 Processing helix chain 'A' and resid 61 through 71 removed outlier: 3.548A pdb=" N CYS A 66 " --> pdb=" O CYS A 62 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 101 removed outlier: 3.507A pdb=" N ILE A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'F' and resid 21 through 46 removed outlier: 3.902A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL F 31 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLU F 43 " --> pdb=" O ALA F 39 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR F 44 " --> pdb=" O ILE F 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 Processing helix chain 'F' and resid 61 through 71 removed outlier: 3.543A pdb=" N CYS F 66 " --> pdb=" O CYS F 62 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP F 68 " --> pdb=" O GLN F 64 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 101 removed outlier: 3.508A pdb=" N ILE F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing helix chain 'B' and resid 21 through 46 removed outlier: 3.920A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU B 43 " --> pdb=" O ALA B 39 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR B 44 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 53 Processing helix chain 'B' and resid 61 through 71 removed outlier: 3.550A pdb=" N CYS B 66 " --> pdb=" O CYS B 62 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASP B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 101 removed outlier: 3.507A pdb=" N ILE B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 removed outlier: 3.633A pdb=" N LYS B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 46 removed outlier: 3.902A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 42 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU C 43 " --> pdb=" O ALA C 39 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR C 44 " --> pdb=" O ILE C 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 53 Processing helix chain 'C' and resid 61 through 71 removed outlier: 3.545A pdb=" N CYS C 66 " --> pdb=" O CYS C 62 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 68 " --> pdb=" O GLN C 64 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ARG C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 101 removed outlier: 3.508A pdb=" N ILE C 84 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 21 through 46 removed outlier: 3.913A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N GLU D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR D 44 " --> pdb=" O ILE D 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 61 through 71 removed outlier: 3.548A pdb=" N CYS D 66 " --> pdb=" O CYS D 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP D 68 " --> pdb=" O GLN D 64 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG D 69 " --> pdb=" O ALA D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 101 removed outlier: 3.508A pdb=" N ILE D 84 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 21 through 46 removed outlier: 3.920A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLU E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR E 44 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 61 through 71 removed outlier: 3.551A pdb=" N CYS E 66 " --> pdb=" O CYS E 62 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP E 68 " --> pdb=" O GLN E 64 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ARG E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 101 removed outlier: 3.507A pdb=" N ILE E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.631A pdb=" N VAL A 54 " --> pdb=" O TYR A 243 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 54 through 55 removed outlier: 3.620A pdb=" N VAL F 54 " --> pdb=" O TYR F 243 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.556A pdb=" N VAL B 54 " --> pdb=" O TYR B 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 removed outlier: 3.619A pdb=" N VAL C 54 " --> pdb=" O TYR C 243 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 54 through 55 removed outlier: 3.632A pdb=" N VAL D 54 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 54 through 55 removed outlier: 3.615A pdb=" N VAL E 54 " --> pdb=" O TYR E 243 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1740 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: 1.33 Time building geometry restraints manager: 1.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2442 1.34 - 1.46: 1875 1.46 - 1.58: 3945 1.58 - 1.70: 0 1.70 - 1.81: 102 Bond restraints: 8364 Sorted by residual: bond pdb=" CA THR A 88 " pdb=" C THR A 88 " ideal model delta sigma weight residual 1.525 1.536 -0.012 1.19e-02 7.06e+03 9.50e-01 bond pdb=" CA THR C 88 " pdb=" C THR C 88 " ideal model delta sigma weight residual 1.525 1.536 -0.011 1.19e-02 7.06e+03 9.27e-01 bond pdb=" CA THR E 88 " pdb=" C THR E 88 " ideal model delta sigma weight residual 1.525 1.536 -0.011 1.19e-02 7.06e+03 9.25e-01 bond pdb=" CA THR D 88 " pdb=" C THR D 88 " ideal model delta sigma weight residual 1.525 1.536 -0.011 1.19e-02 7.06e+03 8.63e-01 bond pdb=" CA THR F 88 " pdb=" C THR F 88 " ideal model delta sigma weight residual 1.525 1.536 -0.011 1.19e-02 7.06e+03 8.58e-01 ... (remaining 8359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 11091 2.13 - 4.26: 165 4.26 - 6.39: 12 6.39 - 8.52: 12 8.52 - 10.65: 6 Bond angle restraints: 11286 Sorted by residual: angle pdb=" CA LEU D 269 " pdb=" CB LEU D 269 " pdb=" CG LEU D 269 " ideal model delta sigma weight residual 116.30 126.95 -10.65 3.50e+00 8.16e-02 9.26e+00 angle pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " pdb=" CG LEU A 269 " ideal model delta sigma weight residual 116.30 126.95 -10.65 3.50e+00 8.16e-02 9.26e+00 angle pdb=" CA LEU C 269 " pdb=" CB LEU C 269 " pdb=" CG LEU C 269 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" CA LEU F 269 " pdb=" CB LEU F 269 " pdb=" CG LEU F 269 " ideal model delta sigma weight residual 116.30 126.92 -10.62 3.50e+00 8.16e-02 9.21e+00 angle pdb=" CA LEU B 269 " pdb=" CB LEU B 269 " pdb=" CG LEU B 269 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.17e+00 ... (remaining 11281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 4132 17.10 - 34.19: 602 34.19 - 51.29: 198 51.29 - 68.39: 0 68.39 - 85.48: 24 Dihedral angle restraints: 4956 sinusoidal: 2040 harmonic: 2916 Sorted by residual: dihedral pdb=" CB CYS C 62 " pdb=" SG CYS C 62 " pdb=" SG CYS C 236 " pdb=" CB CYS C 236 " ideal model delta sinusoidal sigma weight residual 93.00 124.23 -31.23 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS F 62 " pdb=" SG CYS F 62 " pdb=" SG CYS F 236 " pdb=" CB CYS F 236 " ideal model delta sinusoidal sigma weight residual 93.00 124.22 -31.22 1 1.00e+01 1.00e-02 1.39e+01 dihedral pdb=" CB CYS E 62 " pdb=" SG CYS E 62 " pdb=" SG CYS E 236 " pdb=" CB CYS E 236 " ideal model delta sinusoidal sigma weight residual 93.00 124.18 -31.18 1 1.00e+01 1.00e-02 1.39e+01 ... (remaining 4953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 742 0.031 - 0.063: 384 0.063 - 0.094: 123 0.094 - 0.126: 47 0.126 - 0.157: 6 Chirality restraints: 1302 Sorted by residual: chirality pdb=" CA THR F 88 " pdb=" N THR F 88 " pdb=" C THR F 88 " pdb=" CB THR F 88 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA THR E 88 " pdb=" N THR E 88 " pdb=" C THR E 88 " pdb=" CB THR E 88 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA THR B 88 " pdb=" N THR B 88 " pdb=" C THR B 88 " pdb=" CB THR B 88 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 1299 not shown) Planarity restraints: 1374 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG E 246 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C ARG E 246 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG E 246 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO E 247 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 246 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C ARG A 246 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG A 246 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO A 247 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 246 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C ARG F 246 " -0.030 2.00e-02 2.50e+03 pdb=" O ARG F 246 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO F 247 " 0.010 2.00e-02 2.50e+03 ... (remaining 1371 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 762 2.74 - 3.28: 8274 3.28 - 3.82: 13893 3.82 - 4.36: 13597 4.36 - 4.90: 24473 Nonbonded interactions: 60999 Sorted by model distance: nonbonded pdb=" OE2 GLU A 49 " pdb=" OG SER A 245 " model vdw 2.201 3.040 nonbonded pdb=" OE2 GLU D 49 " pdb=" OG SER D 245 " model vdw 2.202 3.040 nonbonded pdb=" OE2 GLU C 49 " pdb=" OG SER C 245 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU F 49 " pdb=" OG SER F 245 " model vdw 2.203 3.040 nonbonded pdb=" OE2 GLU E 49 " pdb=" OG SER E 245 " model vdw 2.209 3.040 ... (remaining 60994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 276 or (resid 401 through 402 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09)))) selection = (chain 'B' and (resid 19 through 276 or (resid 401 through 402 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09)))) selection = (chain 'C' and (resid 19 through 276 or (resid 401 through 402 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09)))) selection = (chain 'D' and (resid 19 through 276 or (resid 401 through 402 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09)))) selection = (chain 'E' and (resid 19 through 276 or (resid 401 through 402 and (name C01 or \ name C02 or name C03 or name C04 or name C05 or name C06 or name C07 or name C08 \ or name C09)))) selection = (chain 'F' and (resid 19 through 401 or (resid 402 and (name C01 or name C02 or \ name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C09 \ )))) } 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 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: 1.490 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.750 Find NCS groups from input model: 0.220 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.003 0.036 8382 Z= 0.141 Angle : 0.700 10.650 11322 Z= 0.344 Chirality : 0.043 0.157 1302 Planarity : 0.003 0.028 1374 Dihedral : 17.482 85.483 3030 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.67 % Allowed : 28.33 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.03 (0.28), residues: 972 helix: 1.37 (0.20), residues: 702 sheet: 1.97 (0.62), residues: 60 loop : -2.05 (0.49), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 206 TYR 0.009 0.001 TYR D 67 PHE 0.009 0.001 PHE E 81 TRP 0.002 0.001 TRP C 79 HIS 0.006 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8364) covalent geometry : angle 0.70085 (11286) SS BOND : bond 0.00086 ( 18) SS BOND : angle 0.56099 ( 36) hydrogen bonds : bond 0.13996 ( 586) hydrogen bonds : angle 5.03567 ( 1740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 372 time to evaluate : 0.339 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 27 LEU cc_start: 0.9161 (pp) cc_final: 0.8955 (pp) REVERT: C 27 LEU cc_start: 0.9152 (pp) cc_final: 0.8949 (pp) REVERT: C 52 MET cc_start: 0.7554 (mmp) cc_final: 0.7257 (mmp) REVERT: D 27 LEU cc_start: 0.9118 (pp) cc_final: 0.8916 (pp) outliers start: 6 outliers final: 0 residues processed: 378 average time/residue: 0.0980 time to fit residues: 49.4286 Evaluate side-chains 237 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS F 82 GLN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.056338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.046296 restraints weight = 41260.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.047924 restraints weight = 23767.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049069 restraints weight = 15834.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.050009 restraints weight = 11717.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.050741 restraints weight = 9136.671| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8382 Z= 0.152 Angle : 0.847 12.030 11322 Z= 0.407 Chirality : 0.047 0.208 1302 Planarity : 0.004 0.028 1374 Dihedral : 5.947 52.266 1248 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.67 % Allowed : 27.00 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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 (0.28), residues: 972 helix: 1.28 (0.19), residues: 744 sheet: 2.17 (0.61), residues: 60 loop : -2.88 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 246 TYR 0.030 0.001 TYR C 234 PHE 0.020 0.001 PHE B 256 TRP 0.010 0.003 TRP E 79 HIS 0.006 0.002 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8364) covalent geometry : angle 0.84776 (11286) SS BOND : bond 0.00224 ( 18) SS BOND : angle 0.28809 ( 36) hydrogen bonds : bond 0.05076 ( 586) hydrogen bonds : angle 4.25399 ( 1740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.354 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: A 27 LEU cc_start: 0.9616 (OUTLIER) cc_final: 0.9415 (pp) REVERT: A 78 TYR cc_start: 0.9423 (t80) cc_final: 0.9062 (t80) REVERT: A 85 MET cc_start: 0.9132 (mmm) cc_final: 0.8814 (mmm) REVERT: A 210 GLU cc_start: 0.9632 (mm-30) cc_final: 0.9225 (tt0) REVERT: A 249 GLU cc_start: 0.9498 (mm-30) cc_final: 0.8955 (mm-30) REVERT: A 271 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9183 (pp20) REVERT: F 78 TYR cc_start: 0.9429 (t80) cc_final: 0.9102 (t80) REVERT: F 85 MET cc_start: 0.9165 (mmm) cc_final: 0.8845 (mmm) REVERT: F 210 GLU cc_start: 0.9648 (mm-30) cc_final: 0.9238 (tt0) REVERT: F 271 GLU cc_start: 0.9444 (tm-30) cc_final: 0.9063 (pp20) REVERT: B 78 TYR cc_start: 0.9403 (t80) cc_final: 0.8994 (t80) REVERT: B 85 MET cc_start: 0.9074 (mmm) cc_final: 0.8800 (mmm) REVERT: B 210 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9288 (tt0) REVERT: B 234 TYR cc_start: 0.8643 (t80) cc_final: 0.8372 (t80) REVERT: B 249 GLU cc_start: 0.9501 (mm-30) cc_final: 0.9202 (mm-30) REVERT: B 271 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9029 (pp20) REVERT: C 78 TYR cc_start: 0.9422 (t80) cc_final: 0.9097 (t80) REVERT: C 85 MET cc_start: 0.9173 (mmm) cc_final: 0.8864 (mmm) REVERT: C 210 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9273 (tt0) REVERT: C 271 GLU cc_start: 0.9441 (tm-30) cc_final: 0.9061 (pp20) REVERT: D 78 TYR cc_start: 0.9414 (t80) cc_final: 0.9052 (t80) REVERT: D 85 MET cc_start: 0.9142 (mmm) cc_final: 0.8823 (mmm) REVERT: D 210 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9223 (tt0) REVERT: D 249 GLU cc_start: 0.9496 (mm-30) cc_final: 0.8952 (mm-30) REVERT: D 271 GLU cc_start: 0.9531 (tm-30) cc_final: 0.9180 (pp20) REVERT: E 78 TYR cc_start: 0.9397 (t80) cc_final: 0.9007 (t80) REVERT: E 85 MET cc_start: 0.9071 (mmm) cc_final: 0.8853 (mmm) REVERT: E 210 GLU cc_start: 0.9651 (mm-30) cc_final: 0.9260 (tt0) REVERT: E 249 GLU cc_start: 0.9514 (mm-30) cc_final: 0.9177 (mm-30) REVERT: E 271 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9036 (pp20) outliers start: 33 outliers final: 2 residues processed: 272 average time/residue: 0.1000 time to fit residues: 36.1960 Evaluate side-chains 257 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain D residue 274 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 69 optimal weight: 8.9990 chunk 92 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045374 restraints weight = 44043.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046957 restraints weight = 24102.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.048115 restraints weight = 15599.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.048985 restraints weight = 11116.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.049633 restraints weight = 8443.710| |-----------------------------------------------------------------------------| r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8382 Z= 0.168 Angle : 0.848 13.299 11322 Z= 0.393 Chirality : 0.045 0.125 1302 Planarity : 0.004 0.024 1374 Dihedral : 5.750 52.213 1248 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.78 % Allowed : 28.67 % Favored : 67.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.01 (0.28), residues: 972 helix: 1.30 (0.19), residues: 750 sheet: 2.11 (0.59), residues: 60 loop : -2.90 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 34 TYR 0.012 0.001 TYR B 243 PHE 0.019 0.001 PHE D 256 TRP 0.015 0.003 TRP F 79 HIS 0.016 0.003 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8364) covalent geometry : angle 0.84892 (11286) SS BOND : bond 0.00256 ( 18) SS BOND : angle 0.36573 ( 36) hydrogen bonds : bond 0.04856 ( 586) hydrogen bonds : angle 4.13245 ( 1740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.326 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: A 49 GLU cc_start: 0.9512 (mp0) cc_final: 0.9082 (mp0) REVERT: A 58 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6362 (mt) REVERT: A 85 MET cc_start: 0.9309 (mmm) cc_final: 0.8979 (mmm) REVERT: A 210 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9273 (tt0) REVERT: A 249 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9057 (mm-30) REVERT: F 58 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6585 (mt) REVERT: F 85 MET cc_start: 0.9312 (mmm) cc_final: 0.8983 (mmm) REVERT: F 210 GLU cc_start: 0.9635 (mm-30) cc_final: 0.9213 (tt0) REVERT: F 271 GLU cc_start: 0.9443 (tm-30) cc_final: 0.8904 (pp20) REVERT: B 52 MET cc_start: 0.8912 (mmm) cc_final: 0.8631 (mmm) REVERT: B 210 GLU cc_start: 0.9662 (mm-30) cc_final: 0.9239 (tt0) REVERT: B 249 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9201 (mm-30) REVERT: B 271 GLU cc_start: 0.9440 (tm-30) cc_final: 0.8888 (pp20) REVERT: C 58 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6458 (mt) REVERT: C 85 MET cc_start: 0.9317 (mmm) cc_final: 0.8997 (mmm) REVERT: C 210 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9283 (tt0) REVERT: C 268 ASN cc_start: 0.9818 (m-40) cc_final: 0.9293 (t0) REVERT: C 271 GLU cc_start: 0.9425 (tm-30) cc_final: 0.8773 (pp20) REVERT: D 58 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6319 (mt) REVERT: D 64 GLN cc_start: 0.9598 (pm20) cc_final: 0.9397 (pm20) REVERT: D 85 MET cc_start: 0.9318 (mmm) cc_final: 0.8987 (mmm) REVERT: D 210 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9271 (tt0) REVERT: D 234 TYR cc_start: 0.8937 (t80) cc_final: 0.8723 (t80) REVERT: D 249 GLU cc_start: 0.9542 (mm-30) cc_final: 0.9056 (mm-30) REVERT: E 58 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6357 (mt) REVERT: E 85 MET cc_start: 0.9274 (mmm) cc_final: 0.9007 (mmm) REVERT: E 210 GLU cc_start: 0.9673 (mm-30) cc_final: 0.9300 (tt0) REVERT: E 234 TYR cc_start: 0.8921 (t80) cc_final: 0.8708 (t80) REVERT: E 249 GLU cc_start: 0.9576 (mm-30) cc_final: 0.9233 (mm-30) REVERT: E 268 ASN cc_start: 0.9841 (m-40) cc_final: 0.9431 (t0) REVERT: E 271 GLU cc_start: 0.9446 (tm-30) cc_final: 0.8789 (pp20) outliers start: 34 outliers final: 16 residues processed: 240 average time/residue: 0.0711 time to fit residues: 25.2992 Evaluate side-chains 225 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 274 HIS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.044532 restraints weight = 45461.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.046087 restraints weight = 25199.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047216 restraints weight = 16485.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048024 restraints weight = 11833.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.048660 restraints weight = 9075.959| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8382 Z= 0.164 Angle : 0.858 14.542 11322 Z= 0.393 Chirality : 0.044 0.123 1302 Planarity : 0.004 0.027 1374 Dihedral : 5.696 53.537 1248 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.89 % Allowed : 29.33 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.16 (0.27), residues: 972 helix: 1.36 (0.19), residues: 750 sheet: 2.37 (0.58), residues: 60 loop : -2.66 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 206 TYR 0.019 0.001 TYR E 78 PHE 0.023 0.001 PHE B 256 TRP 0.035 0.006 TRP F 79 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8364) covalent geometry : angle 0.85930 (11286) SS BOND : bond 0.00274 ( 18) SS BOND : angle 0.40526 ( 36) hydrogen bonds : bond 0.04677 ( 586) hydrogen bonds : angle 4.01547 ( 1740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.387 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: A 49 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9043 (mp0) REVERT: A 58 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6475 (mt) REVERT: A 85 MET cc_start: 0.9378 (mmm) cc_final: 0.9037 (mmm) REVERT: A 206 ARG cc_start: 0.9580 (ptm-80) cc_final: 0.8994 (ptp90) REVERT: A 210 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9276 (tt0) REVERT: A 217 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9156 (tm-30) REVERT: A 249 GLU cc_start: 0.9519 (mm-30) cc_final: 0.8877 (mm-30) REVERT: A 268 ASN cc_start: 0.9845 (OUTLIER) cc_final: 0.9042 (t0) REVERT: F 85 MET cc_start: 0.9404 (mmm) cc_final: 0.9069 (mmm) REVERT: F 206 ARG cc_start: 0.9586 (ptm-80) cc_final: 0.8999 (ptp90) REVERT: F 210 GLU cc_start: 0.9636 (mm-30) cc_final: 0.9266 (tt0) REVERT: F 217 GLN cc_start: 0.9377 (tm-30) cc_final: 0.9104 (tm-30) REVERT: F 271 GLU cc_start: 0.9409 (tm-30) cc_final: 0.9019 (pp20) REVERT: B 48 ASP cc_start: 0.9089 (p0) cc_final: 0.8824 (t0) REVERT: B 52 MET cc_start: 0.9481 (mmm) cc_final: 0.8783 (mmm) REVERT: B 64 GLN cc_start: 0.9554 (pm20) cc_final: 0.9324 (pm20) REVERT: B 85 MET cc_start: 0.9139 (mmm) cc_final: 0.8928 (mmm) REVERT: B 206 ARG cc_start: 0.9554 (ptm-80) cc_final: 0.8925 (ptp90) REVERT: B 210 GLU cc_start: 0.9636 (mm-30) cc_final: 0.9279 (tt0) REVERT: B 249 GLU cc_start: 0.9561 (mm-30) cc_final: 0.8966 (mm-30) REVERT: B 271 GLU cc_start: 0.9423 (tm-30) cc_final: 0.9013 (pp20) REVERT: C 85 MET cc_start: 0.9399 (mmm) cc_final: 0.9053 (mmm) REVERT: C 206 ARG cc_start: 0.9587 (ptm-80) cc_final: 0.9002 (ptp90) REVERT: C 210 GLU cc_start: 0.9631 (mm-30) cc_final: 0.9280 (tt0) REVERT: C 217 GLN cc_start: 0.9373 (tm-30) cc_final: 0.9100 (tm-30) REVERT: C 271 GLU cc_start: 0.9398 (tm-30) cc_final: 0.8980 (pp20) REVERT: D 49 GLU cc_start: 0.9531 (mp0) cc_final: 0.9083 (mp0) REVERT: D 58 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6442 (mt) REVERT: D 85 MET cc_start: 0.9378 (mmm) cc_final: 0.9037 (mmm) REVERT: D 206 ARG cc_start: 0.9588 (ptm-80) cc_final: 0.9001 (ptp90) REVERT: D 210 GLU cc_start: 0.9630 (mm-30) cc_final: 0.9273 (tt0) REVERT: D 217 GLN cc_start: 0.9415 (tm-30) cc_final: 0.9148 (tm-30) REVERT: D 249 GLU cc_start: 0.9516 (mm-30) cc_final: 0.8883 (mm-30) REVERT: D 268 ASN cc_start: 0.9844 (OUTLIER) cc_final: 0.9038 (t0) REVERT: E 64 GLN cc_start: 0.9537 (pm20) cc_final: 0.9307 (pm20) REVERT: E 85 MET cc_start: 0.9324 (mmm) cc_final: 0.9049 (mmm) REVERT: E 206 ARG cc_start: 0.9578 (ptm-80) cc_final: 0.8946 (ptp90) REVERT: E 210 GLU cc_start: 0.9623 (mm-30) cc_final: 0.9232 (tt0) REVERT: E 249 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9224 (mm-30) REVERT: E 254 LEU cc_start: 0.9676 (pp) cc_final: 0.9283 (pp) REVERT: E 257 MET cc_start: 0.8661 (ppp) cc_final: 0.8301 (ppp) REVERT: E 271 GLU cc_start: 0.9425 (tm-30) cc_final: 0.9029 (pp20) outliers start: 44 outliers final: 22 residues processed: 239 average time/residue: 0.0910 time to fit residues: 29.9448 Evaluate side-chains 239 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 212 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 257 MET Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 267 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.0980 chunk 4 optimal weight: 0.0030 chunk 3 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 overall best weight: 1.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** E 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045333 restraints weight = 44312.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046970 restraints weight = 24556.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.048103 restraints weight = 16026.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048959 restraints weight = 11536.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.049598 restraints weight = 8855.495| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8382 Z= 0.135 Angle : 0.871 13.648 11322 Z= 0.388 Chirality : 0.044 0.151 1302 Planarity : 0.004 0.026 1374 Dihedral : 5.439 53.175 1248 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 3.56 % Allowed : 27.67 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.01 (0.27), residues: 972 helix: 1.20 (0.19), residues: 750 sheet: 2.56 (0.59), residues: 60 loop : -2.57 (0.46), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 206 TYR 0.015 0.001 TYR E 78 PHE 0.021 0.001 PHE F 256 TRP 0.051 0.007 TRP A 79 HIS 0.006 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8364) covalent geometry : angle 0.87188 (11286) SS BOND : bond 0.00184 ( 18) SS BOND : angle 0.36942 ( 36) hydrogen bonds : bond 0.04489 ( 586) hydrogen bonds : angle 4.02066 ( 1740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 242 time to evaluate : 0.333 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: A 49 GLU cc_start: 0.9534 (OUTLIER) cc_final: 0.9038 (mp0) REVERT: A 82 GLN cc_start: 0.9381 (tp40) cc_final: 0.9116 (tp40) REVERT: A 85 MET cc_start: 0.9360 (mmm) cc_final: 0.8971 (mmm) REVERT: A 206 ARG cc_start: 0.9570 (ptm-80) cc_final: 0.8966 (ptp90) REVERT: A 210 GLU cc_start: 0.9641 (mm-30) cc_final: 0.9221 (tt0) REVERT: A 217 GLN cc_start: 0.9454 (tm-30) cc_final: 0.9077 (tm-30) REVERT: A 249 GLU cc_start: 0.9499 (mm-30) cc_final: 0.8833 (mm-30) REVERT: A 254 LEU cc_start: 0.9635 (pp) cc_final: 0.9302 (pp) REVERT: A 257 MET cc_start: 0.8690 (ppp) cc_final: 0.8341 (ppp) REVERT: A 268 ASN cc_start: 0.9823 (OUTLIER) cc_final: 0.8697 (t0) REVERT: A 271 GLU cc_start: 0.9372 (tm-30) cc_final: 0.8970 (pp20) REVERT: F 48 ASP cc_start: 0.9276 (p0) cc_final: 0.9031 (p0) REVERT: F 49 GLU cc_start: 0.9634 (mp0) cc_final: 0.9332 (mp0) REVERT: F 85 MET cc_start: 0.9384 (mmm) cc_final: 0.9022 (mmm) REVERT: F 206 ARG cc_start: 0.9594 (ptm-80) cc_final: 0.9004 (ptp90) REVERT: F 210 GLU cc_start: 0.9642 (mm-30) cc_final: 0.9248 (tt0) REVERT: F 217 GLN cc_start: 0.9425 (tm-30) cc_final: 0.9090 (tm-30) REVERT: F 271 GLU cc_start: 0.9383 (tm-30) cc_final: 0.8885 (pp20) REVERT: B 48 ASP cc_start: 0.9239 (p0) cc_final: 0.8835 (t0) REVERT: B 49 GLU cc_start: 0.9469 (mp0) cc_final: 0.9245 (mp0) REVERT: B 52 MET cc_start: 0.9658 (mmm) cc_final: 0.9277 (mmm) REVERT: B 85 MET cc_start: 0.9267 (mmm) cc_final: 0.8974 (mmm) REVERT: B 206 ARG cc_start: 0.9567 (ptm-80) cc_final: 0.8935 (ptp90) REVERT: B 210 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9235 (tt0) REVERT: B 249 GLU cc_start: 0.9544 (mm-30) cc_final: 0.9090 (mm-30) REVERT: B 250 LYS cc_start: 0.9702 (mmtt) cc_final: 0.9464 (mmtt) REVERT: C 85 MET cc_start: 0.9397 (mmm) cc_final: 0.9029 (mmm) REVERT: C 206 ARG cc_start: 0.9588 (ptm-80) cc_final: 0.8992 (ptp90) REVERT: C 210 GLU cc_start: 0.9653 (mm-30) cc_final: 0.9285 (tt0) REVERT: C 217 GLN cc_start: 0.9432 (tm-30) cc_final: 0.9099 (tm-30) REVERT: C 271 GLU cc_start: 0.9377 (tm-30) cc_final: 0.8892 (pp20) REVERT: D 82 GLN cc_start: 0.9384 (tp40) cc_final: 0.9114 (tp40) REVERT: D 85 MET cc_start: 0.9359 (mmm) cc_final: 0.8972 (mmm) REVERT: D 206 ARG cc_start: 0.9570 (ptm-80) cc_final: 0.8972 (ptp90) REVERT: D 210 GLU cc_start: 0.9640 (mm-30) cc_final: 0.9219 (tt0) REVERT: D 217 GLN cc_start: 0.9454 (tm-30) cc_final: 0.9075 (tm-30) REVERT: D 249 GLU cc_start: 0.9510 (mm-30) cc_final: 0.8922 (mm-30) REVERT: D 254 LEU cc_start: 0.9639 (pp) cc_final: 0.9311 (pp) REVERT: D 257 MET cc_start: 0.8697 (ppp) cc_final: 0.8344 (ppp) REVERT: D 268 ASN cc_start: 0.9814 (OUTLIER) cc_final: 0.8714 (t0) REVERT: D 271 GLU cc_start: 0.9377 (tm-30) cc_final: 0.8977 (pp20) REVERT: E 85 MET cc_start: 0.9327 (mmm) cc_final: 0.8991 (mmm) REVERT: E 206 ARG cc_start: 0.9570 (ptm-80) cc_final: 0.8946 (ptp90) REVERT: E 210 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9226 (tt0) REVERT: E 249 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9190 (mm-30) REVERT: E 254 LEU cc_start: 0.9616 (pp) cc_final: 0.9255 (pp) REVERT: E 257 MET cc_start: 0.8653 (ppp) cc_final: 0.8233 (ppp) REVERT: E 271 GLU cc_start: 0.9372 (tm-30) cc_final: 0.8874 (pp20) outliers start: 32 outliers final: 15 residues processed: 264 average time/residue: 0.0925 time to fit residues: 33.3996 Evaluate side-chains 238 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 257 MET Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 92 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.055673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.046071 restraints weight = 42626.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047742 restraints weight = 24079.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.048932 restraints weight = 15812.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.049800 restraints weight = 11479.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.050482 restraints weight = 8960.253| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8382 Z= 0.138 Angle : 0.883 13.357 11322 Z= 0.392 Chirality : 0.044 0.199 1302 Planarity : 0.004 0.029 1374 Dihedral : 5.393 53.482 1248 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.89 % Allowed : 29.44 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.77 (0.27), residues: 972 helix: 1.25 (0.19), residues: 714 sheet: 2.60 (0.57), residues: 60 loop : -2.97 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 77 TYR 0.012 0.001 TYR E 78 PHE 0.026 0.001 PHE E 256 TRP 0.050 0.010 TRP E 79 HIS 0.005 0.001 HIS C 75 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8364) covalent geometry : angle 0.88388 (11286) SS BOND : bond 0.00198 ( 18) SS BOND : angle 0.48888 ( 36) hydrogen bonds : bond 0.04432 ( 586) hydrogen bonds : angle 4.08868 ( 1740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.297 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: A 49 GLU cc_start: 0.9567 (OUTLIER) cc_final: 0.9059 (mp0) REVERT: A 82 GLN cc_start: 0.9295 (tp40) cc_final: 0.9028 (tp40) REVERT: A 85 MET cc_start: 0.9409 (mmm) cc_final: 0.9020 (mmm) REVERT: A 206 ARG cc_start: 0.9572 (ptm-80) cc_final: 0.8972 (ptp90) REVERT: A 210 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9247 (tt0) REVERT: A 217 GLN cc_start: 0.9447 (tm-30) cc_final: 0.9060 (tm-30) REVERT: A 249 GLU cc_start: 0.9500 (mm-30) cc_final: 0.8930 (mm-30) REVERT: A 254 LEU cc_start: 0.9569 (pp) cc_final: 0.9260 (pp) REVERT: A 257 MET cc_start: 0.8584 (ppp) cc_final: 0.8330 (ppp) REVERT: A 268 ASN cc_start: 0.9819 (OUTLIER) cc_final: 0.9088 (t0) REVERT: F 85 MET cc_start: 0.9430 (mmm) cc_final: 0.9072 (mmm) REVERT: F 206 ARG cc_start: 0.9593 (ptm-80) cc_final: 0.9000 (ptp90) REVERT: F 210 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9275 (tt0) REVERT: F 217 GLN cc_start: 0.9451 (tm-30) cc_final: 0.9104 (tm-30) REVERT: F 271 GLU cc_start: 0.9407 (tm-30) cc_final: 0.8950 (pp20) REVERT: B 48 ASP cc_start: 0.9255 (p0) cc_final: 0.8835 (t0) REVERT: B 52 MET cc_start: 0.9672 (mmm) cc_final: 0.9111 (mmm) REVERT: B 85 MET cc_start: 0.9365 (mmm) cc_final: 0.9078 (mmm) REVERT: B 206 ARG cc_start: 0.9586 (ptm-80) cc_final: 0.8959 (ptp90) REVERT: B 210 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9270 (tt0) REVERT: B 249 GLU cc_start: 0.9552 (mm-30) cc_final: 0.9108 (mm-30) REVERT: B 271 GLU cc_start: 0.9376 (tm-30) cc_final: 0.8817 (pp20) REVERT: C 85 MET cc_start: 0.9430 (mmm) cc_final: 0.9069 (mmm) REVERT: C 206 ARG cc_start: 0.9590 (ptm-80) cc_final: 0.9021 (ptp90) REVERT: C 210 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9326 (tt0) REVERT: C 217 GLN cc_start: 0.9466 (tm-30) cc_final: 0.9139 (tm-30) REVERT: C 271 GLU cc_start: 0.9400 (tm-30) cc_final: 0.8990 (pp20) REVERT: D 48 ASP cc_start: 0.9065 (p0) cc_final: 0.8604 (t0) REVERT: D 49 GLU cc_start: 0.9394 (mp0) cc_final: 0.9001 (mp0) REVERT: D 52 MET cc_start: 0.9419 (mmm) cc_final: 0.8735 (mmm) REVERT: D 82 GLN cc_start: 0.9313 (tp40) cc_final: 0.9042 (tp40) REVERT: D 85 MET cc_start: 0.9432 (mmm) cc_final: 0.9042 (mmm) REVERT: D 206 ARG cc_start: 0.9559 (ptm-80) cc_final: 0.8933 (ptp90) REVERT: D 210 GLU cc_start: 0.9665 (mm-30) cc_final: 0.9351 (tt0) REVERT: D 217 GLN cc_start: 0.9442 (tm-30) cc_final: 0.9057 (tm-30) REVERT: D 249 GLU cc_start: 0.9493 (mm-30) cc_final: 0.8951 (mm-30) REVERT: D 254 LEU cc_start: 0.9570 (pp) cc_final: 0.9260 (pp) REVERT: D 257 MET cc_start: 0.8581 (ppp) cc_final: 0.8327 (ppp) REVERT: D 268 ASN cc_start: 0.9788 (OUTLIER) cc_final: 0.9067 (t0) REVERT: E 85 MET cc_start: 0.9409 (mmm) cc_final: 0.9081 (mmm) REVERT: E 206 ARG cc_start: 0.9581 (ptm-80) cc_final: 0.8975 (ptp90) REVERT: E 210 GLU cc_start: 0.9626 (mm-30) cc_final: 0.9246 (tt0) REVERT: E 249 GLU cc_start: 0.9515 (mm-30) cc_final: 0.9209 (mm-30) REVERT: E 254 LEU cc_start: 0.9587 (pp) cc_final: 0.9273 (pp) REVERT: E 257 MET cc_start: 0.8611 (ppp) cc_final: 0.8166 (ppp) REVERT: E 271 GLU cc_start: 0.9380 (tm-30) cc_final: 0.8845 (pp20) outliers start: 26 outliers final: 15 residues processed: 242 average time/residue: 0.0873 time to fit residues: 29.0280 Evaluate side-chains 235 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 257 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN ** F 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 274 HIS ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN E 274 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.057192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047313 restraints weight = 42399.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049083 restraints weight = 23076.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050366 restraints weight = 14857.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051265 restraints weight = 10622.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051956 restraints weight = 8130.727| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8382 Z= 0.138 Angle : 0.922 13.557 11322 Z= 0.408 Chirality : 0.045 0.152 1302 Planarity : 0.004 0.029 1374 Dihedral : 5.361 53.635 1248 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.00 % Allowed : 30.44 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.85 (0.27), residues: 972 helix: 1.30 (0.19), residues: 714 sheet: 2.65 (0.56), residues: 60 loop : -2.91 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 233 TYR 0.011 0.001 TYR E 78 PHE 0.024 0.001 PHE E 256 TRP 0.055 0.011 TRP F 79 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8364) covalent geometry : angle 0.92296 (11286) SS BOND : bond 0.00188 ( 18) SS BOND : angle 0.40184 ( 36) hydrogen bonds : bond 0.04342 ( 586) hydrogen bonds : angle 4.07343 ( 1740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 219 time to evaluate : 0.327 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: A 49 GLU cc_start: 0.9578 (OUTLIER) cc_final: 0.9058 (mp0) REVERT: A 82 GLN cc_start: 0.9207 (tp40) cc_final: 0.8967 (tp40) REVERT: A 85 MET cc_start: 0.9425 (mmm) cc_final: 0.9014 (mmm) REVERT: A 206 ARG cc_start: 0.9578 (ptm-80) cc_final: 0.8968 (ptp90) REVERT: A 210 GLU cc_start: 0.9669 (mm-30) cc_final: 0.9255 (tt0) REVERT: A 217 GLN cc_start: 0.9443 (tm-30) cc_final: 0.9057 (tm-30) REVERT: A 249 GLU cc_start: 0.9465 (mm-30) cc_final: 0.8924 (mm-30) REVERT: A 254 LEU cc_start: 0.9475 (pp) cc_final: 0.9234 (pp) REVERT: A 257 MET cc_start: 0.8414 (ppp) cc_final: 0.8167 (ppp) REVERT: A 268 ASN cc_start: 0.9793 (OUTLIER) cc_final: 0.9044 (t0) REVERT: F 85 MET cc_start: 0.9456 (mmm) cc_final: 0.9122 (mmm) REVERT: F 206 ARG cc_start: 0.9597 (ptm-80) cc_final: 0.9048 (ptp90) REVERT: F 210 GLU cc_start: 0.9634 (mm-30) cc_final: 0.9267 (tt0) REVERT: F 217 GLN cc_start: 0.9432 (tm-30) cc_final: 0.9091 (tm-30) REVERT: F 271 GLU cc_start: 0.9396 (tm-30) cc_final: 0.8884 (pp20) REVERT: B 48 ASP cc_start: 0.9198 (p0) cc_final: 0.8802 (t0) REVERT: B 52 MET cc_start: 0.9660 (mmm) cc_final: 0.9077 (mmm) REVERT: B 85 MET cc_start: 0.9381 (mmm) cc_final: 0.9073 (mmm) REVERT: B 206 ARG cc_start: 0.9600 (ptm-80) cc_final: 0.8987 (ptp90) REVERT: B 210 GLU cc_start: 0.9627 (mm-30) cc_final: 0.9282 (tt0) REVERT: B 249 GLU cc_start: 0.9539 (mm-30) cc_final: 0.9170 (mm-30) REVERT: C 48 ASP cc_start: 0.8933 (p0) cc_final: 0.8629 (t0) REVERT: C 52 MET cc_start: 0.9493 (mmm) cc_final: 0.8796 (mmm) REVERT: C 64 GLN cc_start: 0.9605 (pm20) cc_final: 0.9371 (pm20) REVERT: C 85 MET cc_start: 0.9471 (mmm) cc_final: 0.9117 (mmm) REVERT: C 206 ARG cc_start: 0.9599 (ptm-80) cc_final: 0.9004 (ptp90) REVERT: C 210 GLU cc_start: 0.9654 (mm-30) cc_final: 0.9267 (tt0) REVERT: C 217 GLN cc_start: 0.9453 (tm-30) cc_final: 0.9143 (tm-30) REVERT: C 271 GLU cc_start: 0.9391 (tm-30) cc_final: 0.8885 (pp20) REVERT: D 48 ASP cc_start: 0.9057 (p0) cc_final: 0.8542 (t0) REVERT: D 52 MET cc_start: 0.9416 (mmm) cc_final: 0.8703 (mmm) REVERT: D 82 GLN cc_start: 0.9201 (tp40) cc_final: 0.8953 (tp40) REVERT: D 85 MET cc_start: 0.9437 (mmm) cc_final: 0.9029 (mmm) REVERT: D 206 ARG cc_start: 0.9580 (ptm-80) cc_final: 0.8973 (ptp90) REVERT: D 210 GLU cc_start: 0.9670 (mm-30) cc_final: 0.9243 (tt0) REVERT: D 217 GLN cc_start: 0.9438 (tm-30) cc_final: 0.9050 (tm-30) REVERT: D 249 GLU cc_start: 0.9431 (mm-30) cc_final: 0.9040 (mm-30) REVERT: D 254 LEU cc_start: 0.9458 (pp) cc_final: 0.9215 (pp) REVERT: D 257 MET cc_start: 0.8396 (ppp) cc_final: 0.8164 (ppp) REVERT: D 268 ASN cc_start: 0.9794 (OUTLIER) cc_final: 0.9044 (t0) REVERT: E 48 ASP cc_start: 0.8990 (p0) cc_final: 0.8766 (t0) REVERT: E 52 MET cc_start: 0.9546 (mmm) cc_final: 0.8689 (mmm) REVERT: E 85 MET cc_start: 0.9452 (mmm) cc_final: 0.9094 (mmm) REVERT: E 206 ARG cc_start: 0.9594 (ptm-80) cc_final: 0.8786 (ptp90) REVERT: E 249 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9241 (mm-30) outliers start: 27 outliers final: 17 residues processed: 238 average time/residue: 0.0865 time to fit residues: 28.2766 Evaluate side-chains 231 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 274 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.056708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.046908 restraints weight = 42333.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048670 restraints weight = 23222.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.049833 restraints weight = 14923.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.050736 restraints weight = 10936.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051429 restraints weight = 8389.064| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8382 Z= 0.148 Angle : 0.964 13.651 11322 Z= 0.430 Chirality : 0.047 0.254 1302 Planarity : 0.004 0.032 1374 Dihedral : 5.474 54.553 1248 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.56 % Allowed : 30.22 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.82 (0.27), residues: 972 helix: 1.28 (0.19), residues: 714 sheet: 2.63 (0.55), residues: 60 loop : -2.93 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 77 TYR 0.030 0.001 TYR A 234 PHE 0.026 0.001 PHE F 256 TRP 0.055 0.007 TRP F 79 HIS 0.005 0.001 HIS A 75 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8364) covalent geometry : angle 0.96491 (11286) SS BOND : bond 0.00215 ( 18) SS BOND : angle 0.39988 ( 36) hydrogen bonds : bond 0.04408 ( 586) hydrogen bonds : angle 4.16102 ( 1740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 218 time to evaluate : 0.387 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: A 49 GLU cc_start: 0.9577 (OUTLIER) cc_final: 0.9049 (mp0) REVERT: A 68 ASP cc_start: 0.9450 (p0) cc_final: 0.8571 (t70) REVERT: A 82 GLN cc_start: 0.9232 (tp40) cc_final: 0.8936 (tp40) REVERT: A 85 MET cc_start: 0.9456 (mmm) cc_final: 0.9025 (mmm) REVERT: A 206 ARG cc_start: 0.9571 (ptm-80) cc_final: 0.8978 (ptp90) REVERT: A 210 GLU cc_start: 0.9666 (mm-30) cc_final: 0.9275 (tt0) REVERT: A 217 GLN cc_start: 0.9444 (tm-30) cc_final: 0.8951 (tm-30) REVERT: A 268 ASN cc_start: 0.9779 (OUTLIER) cc_final: 0.8685 (t0) REVERT: A 271 GLU cc_start: 0.9461 (tm-30) cc_final: 0.8966 (pp20) REVERT: F 85 MET cc_start: 0.9482 (mmm) cc_final: 0.9119 (mmm) REVERT: F 206 ARG cc_start: 0.9604 (ptm-80) cc_final: 0.9017 (ptp90) REVERT: F 210 GLU cc_start: 0.9647 (mm-30) cc_final: 0.9321 (tt0) REVERT: F 217 GLN cc_start: 0.9357 (tm-30) cc_final: 0.8898 (tm-30) REVERT: B 48 ASP cc_start: 0.9162 (p0) cc_final: 0.8739 (t0) REVERT: B 52 MET cc_start: 0.9651 (mmm) cc_final: 0.9033 (mmm) REVERT: B 58 LEU cc_start: 0.6687 (OUTLIER) cc_final: 0.6415 (mt) REVERT: B 85 MET cc_start: 0.9422 (mmm) cc_final: 0.9109 (mmm) REVERT: B 206 ARG cc_start: 0.9607 (ptm-80) cc_final: 0.8791 (ptp90) REVERT: B 249 GLU cc_start: 0.9516 (mm-30) cc_final: 0.9162 (mm-30) REVERT: B 271 GLU cc_start: 0.9473 (tm-30) cc_final: 0.9017 (pp20) REVERT: C 48 ASP cc_start: 0.8923 (p0) cc_final: 0.8581 (t0) REVERT: C 52 MET cc_start: 0.9524 (mmm) cc_final: 0.8760 (mmm) REVERT: C 58 LEU cc_start: 0.6221 (OUTLIER) cc_final: 0.5996 (mt) REVERT: C 85 MET cc_start: 0.9483 (mmm) cc_final: 0.9120 (mmm) REVERT: C 205 PHE cc_start: 0.9583 (OUTLIER) cc_final: 0.9380 (m-10) REVERT: C 206 ARG cc_start: 0.9597 (ptm-80) cc_final: 0.9022 (ptp90) REVERT: C 210 GLU cc_start: 0.9663 (mm-30) cc_final: 0.9326 (tt0) REVERT: C 217 GLN cc_start: 0.9444 (tm-30) cc_final: 0.9111 (tm-30) REVERT: C 271 GLU cc_start: 0.9436 (tm-30) cc_final: 0.8932 (pp20) REVERT: D 48 ASP cc_start: 0.9152 (p0) cc_final: 0.8662 (t0) REVERT: D 49 GLU cc_start: 0.9348 (mp0) cc_final: 0.9113 (mp0) REVERT: D 52 MET cc_start: 0.9422 (mmm) cc_final: 0.8702 (mmm) REVERT: D 82 GLN cc_start: 0.9218 (tp40) cc_final: 0.8927 (tp40) REVERT: D 85 MET cc_start: 0.9464 (mmm) cc_final: 0.9038 (mmm) REVERT: D 206 ARG cc_start: 0.9576 (ptm-80) cc_final: 0.8978 (ptp90) REVERT: D 210 GLU cc_start: 0.9675 (mm-30) cc_final: 0.9269 (tt0) REVERT: D 217 GLN cc_start: 0.9446 (tm-30) cc_final: 0.8953 (tm-30) REVERT: D 268 ASN cc_start: 0.9854 (OUTLIER) cc_final: 0.8878 (t0) REVERT: D 271 GLU cc_start: 0.9484 (tm-30) cc_final: 0.8995 (pp20) REVERT: E 48 ASP cc_start: 0.9052 (p0) cc_final: 0.8801 (t0) REVERT: E 52 MET cc_start: 0.9557 (mmm) cc_final: 0.8818 (mmm) REVERT: E 58 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6490 (mt) REVERT: E 85 MET cc_start: 0.9479 (mmm) cc_final: 0.9087 (mmm) REVERT: E 206 ARG cc_start: 0.9488 (ptm-80) cc_final: 0.8975 (ptp90) REVERT: E 249 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9224 (mm-30) REVERT: E 271 GLU cc_start: 0.9462 (tm-30) cc_final: 0.8970 (pp20) outliers start: 23 outliers final: 14 residues processed: 233 average time/residue: 0.0896 time to fit residues: 28.7517 Evaluate side-chains 232 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 66 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.054875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.045506 restraints weight = 43078.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047224 restraints weight = 23212.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.048466 restraints weight = 14870.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.049361 restraints weight = 10559.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.050060 restraints weight = 8042.262| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.6025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8382 Z= 0.176 Angle : 0.986 14.272 11322 Z= 0.444 Chirality : 0.047 0.246 1302 Planarity : 0.004 0.035 1374 Dihedral : 5.795 56.694 1248 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.78 % Allowed : 30.89 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.81 (0.27), residues: 972 helix: 1.31 (0.19), residues: 714 sheet: 2.69 (0.55), residues: 60 loop : -3.11 (0.41), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 233 TYR 0.009 0.001 TYR E 78 PHE 0.022 0.001 PHE D 256 TRP 0.068 0.006 TRP E 79 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 8364) covalent geometry : angle 0.98745 (11286) SS BOND : bond 0.00308 ( 18) SS BOND : angle 0.51128 ( 36) hydrogen bonds : bond 0.04597 ( 586) hydrogen bonds : angle 4.21892 ( 1740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.352 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: A 68 ASP cc_start: 0.9438 (p0) cc_final: 0.8438 (t70) REVERT: A 82 GLN cc_start: 0.9339 (tp40) cc_final: 0.8976 (tp40) REVERT: A 85 MET cc_start: 0.9478 (mmm) cc_final: 0.9068 (mmm) REVERT: A 206 ARG cc_start: 0.9567 (ptm-80) cc_final: 0.8958 (ptp90) REVERT: A 210 GLU cc_start: 0.9661 (mm-30) cc_final: 0.9253 (tt0) REVERT: A 217 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9063 (tm-30) REVERT: A 268 ASN cc_start: 0.9784 (OUTLIER) cc_final: 0.8727 (t0) REVERT: A 271 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9035 (pp20) REVERT: F 48 ASP cc_start: 0.8920 (p0) cc_final: 0.8320 (t0) REVERT: F 85 MET cc_start: 0.9522 (mmm) cc_final: 0.9107 (mmm) REVERT: F 206 ARG cc_start: 0.9611 (ptm-80) cc_final: 0.8793 (ptp90) REVERT: F 217 GLN cc_start: 0.9480 (tm-30) cc_final: 0.9172 (tm-30) REVERT: F 271 GLU cc_start: 0.9547 (tm-30) cc_final: 0.9146 (pp20) REVERT: B 48 ASP cc_start: 0.9192 (p0) cc_final: 0.8781 (t0) REVERT: B 52 MET cc_start: 0.9659 (mmm) cc_final: 0.9059 (mmm) REVERT: B 58 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6309 (mt) REVERT: B 85 MET cc_start: 0.9474 (mmm) cc_final: 0.9089 (mmm) REVERT: B 206 ARG cc_start: 0.9490 (ptm-80) cc_final: 0.8943 (ptp90) REVERT: B 271 GLU cc_start: 0.9545 (tm-30) cc_final: 0.9056 (pp20) REVERT: C 48 ASP cc_start: 0.8906 (p0) cc_final: 0.8564 (t0) REVERT: C 52 MET cc_start: 0.9563 (mmm) cc_final: 0.8825 (mmm) REVERT: C 58 LEU cc_start: 0.6145 (OUTLIER) cc_final: 0.5934 (mt) REVERT: C 85 MET cc_start: 0.9506 (mmm) cc_final: 0.9083 (mmm) REVERT: C 205 PHE cc_start: 0.9612 (OUTLIER) cc_final: 0.9410 (m-10) REVERT: C 206 ARG cc_start: 0.9596 (ptm-80) cc_final: 0.8781 (ptp90) REVERT: D 48 ASP cc_start: 0.9240 (p0) cc_final: 0.8806 (t0) REVERT: D 49 GLU cc_start: 0.9403 (mp0) cc_final: 0.9112 (mp0) REVERT: D 52 MET cc_start: 0.9393 (mmm) cc_final: 0.8705 (mmm) REVERT: D 64 GLN cc_start: 0.9483 (pm20) cc_final: 0.9246 (pm20) REVERT: D 82 GLN cc_start: 0.9318 (tp40) cc_final: 0.8929 (tp-100) REVERT: D 85 MET cc_start: 0.9493 (mmm) cc_final: 0.9075 (mmm) REVERT: D 206 ARG cc_start: 0.9569 (ptm-80) cc_final: 0.8993 (ptp90) REVERT: D 210 GLU cc_start: 0.9671 (mm-30) cc_final: 0.9277 (tt0) REVERT: D 217 GLN cc_start: 0.9399 (tm-30) cc_final: 0.9052 (tm-30) REVERT: D 271 GLU cc_start: 0.9498 (tm-30) cc_final: 0.9058 (pp20) REVERT: E 52 MET cc_start: 0.9554 (mmm) cc_final: 0.8807 (mmm) REVERT: E 58 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.6147 (mt) REVERT: E 79 TRP cc_start: 0.8547 (m100) cc_final: 0.8077 (m100) REVERT: E 85 MET cc_start: 0.9505 (mmm) cc_final: 0.9088 (mmm) REVERT: E 206 ARG cc_start: 0.9596 (ptm-80) cc_final: 0.8968 (ptp90) REVERT: E 249 GLU cc_start: 0.9505 (mm-30) cc_final: 0.9200 (mm-30) REVERT: E 271 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9035 (pp20) outliers start: 25 outliers final: 17 residues processed: 224 average time/residue: 0.0779 time to fit residues: 24.7730 Evaluate side-chains 230 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 208 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 205 PHE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.055176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045546 restraints weight = 42650.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047240 restraints weight = 23884.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048469 restraints weight = 15705.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.049360 restraints weight = 11356.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.050051 restraints weight = 8744.740| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.6117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8382 Z= 0.155 Angle : 1.027 14.788 11322 Z= 0.456 Chirality : 0.048 0.250 1302 Planarity : 0.004 0.036 1374 Dihedral : 5.765 56.900 1248 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.44 % Allowed : 31.44 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.98 (0.27), residues: 972 helix: 1.45 (0.19), residues: 678 sheet: 2.92 (0.56), residues: 60 loop : -2.45 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 233 TYR 0.008 0.001 TYR B 78 PHE 0.024 0.001 PHE A 256 TRP 0.077 0.007 TRP F 79 HIS 0.005 0.002 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 8364) covalent geometry : angle 1.02808 (11286) SS BOND : bond 0.00220 ( 18) SS BOND : angle 0.44440 ( 36) hydrogen bonds : bond 0.04624 ( 586) hydrogen bonds : angle 4.24891 ( 1740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1944 Ramachandran restraints generated. 972 Oldfield, 0 Emsley, 972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 217 time to evaluate : 0.317 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: A 68 ASP cc_start: 0.9428 (p0) cc_final: 0.8495 (t70) REVERT: A 82 GLN cc_start: 0.9256 (tp40) cc_final: 0.8869 (tp40) REVERT: A 85 MET cc_start: 0.9459 (mmm) cc_final: 0.9044 (mmm) REVERT: A 206 ARG cc_start: 0.9561 (ptm-80) cc_final: 0.8925 (ptp90) REVERT: A 217 GLN cc_start: 0.9354 (tm-30) cc_final: 0.9040 (tm-30) REVERT: A 271 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9050 (pp20) REVERT: F 48 ASP cc_start: 0.8909 (p0) cc_final: 0.8350 (t0) REVERT: F 79 TRP cc_start: 0.8157 (m100) cc_final: 0.7223 (m100) REVERT: F 85 MET cc_start: 0.9510 (mmm) cc_final: 0.9102 (mmm) REVERT: F 206 ARG cc_start: 0.9447 (ptm-80) cc_final: 0.8983 (ptp90) REVERT: F 217 GLN cc_start: 0.9526 (tm-30) cc_final: 0.9220 (pp30) REVERT: F 257 MET cc_start: 0.8868 (ttt) cc_final: 0.8654 (mmm) REVERT: F 271 GLU cc_start: 0.9530 (tm-30) cc_final: 0.9034 (pp20) REVERT: B 48 ASP cc_start: 0.9236 (p0) cc_final: 0.8751 (t0) REVERT: B 52 MET cc_start: 0.9655 (mmm) cc_final: 0.9070 (mmm) REVERT: B 58 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6259 (mt) REVERT: B 85 MET cc_start: 0.9438 (mmm) cc_final: 0.9045 (mmm) REVERT: B 206 ARG cc_start: 0.9575 (ptm-80) cc_final: 0.8915 (ptp90) REVERT: B 249 GLU cc_start: 0.9519 (mm-30) cc_final: 0.9149 (mm-30) REVERT: B 271 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9012 (pp20) REVERT: C 48 ASP cc_start: 0.8891 (p0) cc_final: 0.8503 (t0) REVERT: C 52 MET cc_start: 0.9572 (mmm) cc_final: 0.8794 (mmm) REVERT: C 58 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5790 (mt) REVERT: C 85 MET cc_start: 0.9503 (mmm) cc_final: 0.9070 (mmm) REVERT: C 206 ARG cc_start: 0.9448 (ptm-80) cc_final: 0.8981 (ptp90) REVERT: C 271 GLU cc_start: 0.9559 (tm-30) cc_final: 0.9081 (pp20) REVERT: D 48 ASP cc_start: 0.9254 (p0) cc_final: 0.8773 (t0) REVERT: D 49 GLU cc_start: 0.9421 (mp0) cc_final: 0.9183 (mp0) REVERT: D 52 MET cc_start: 0.9399 (mmm) cc_final: 0.8729 (mmm) REVERT: D 64 GLN cc_start: 0.9484 (pm20) cc_final: 0.9254 (pm20) REVERT: D 82 GLN cc_start: 0.9239 (tp40) cc_final: 0.9006 (tp40) REVERT: D 85 MET cc_start: 0.9473 (mmm) cc_final: 0.9043 (mmm) REVERT: D 206 ARG cc_start: 0.9571 (ptm-80) cc_final: 0.8920 (ptp90) REVERT: D 210 GLU cc_start: 0.9672 (mm-30) cc_final: 0.9364 (tt0) REVERT: D 217 GLN cc_start: 0.9406 (tm-30) cc_final: 0.9075 (tm-30) REVERT: D 268 ASN cc_start: 0.9806 (OUTLIER) cc_final: 0.8797 (t0) REVERT: D 271 GLU cc_start: 0.9504 (tm-30) cc_final: 0.9029 (pp20) REVERT: E 48 ASP cc_start: 0.8867 (t0) cc_final: 0.8538 (t0) REVERT: E 58 LEU cc_start: 0.6212 (OUTLIER) cc_final: 0.5974 (mt) REVERT: E 85 MET cc_start: 0.9488 (mmm) cc_final: 0.9062 (mmm) REVERT: E 206 ARG cc_start: 0.9596 (ptm-80) cc_final: 0.8944 (ptp90) REVERT: E 249 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9225 (mm-30) REVERT: E 271 GLU cc_start: 0.9507 (tm-30) cc_final: 0.9017 (pp20) outliers start: 22 outliers final: 18 residues processed: 229 average time/residue: 0.0918 time to fit residues: 28.8970 Evaluate side-chains 235 residues out of total 900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.0170 chunk 47 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 0.0970 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.056285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.046540 restraints weight = 42430.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048303 restraints weight = 22873.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.049633 restraints weight = 14638.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.050565 restraints weight = 10383.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.051289 restraints weight = 7859.757| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8382 Z= 0.153 Angle : 1.028 14.693 11322 Z= 0.458 Chirality : 0.048 0.245 1302 Planarity : 0.004 0.037 1374 Dihedral : 5.759 57.048 1248 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.11 % Allowed : 32.11 % Favored : 65.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.84 (0.27), residues: 972 helix: 1.34 (0.19), residues: 678 sheet: 2.88 (0.55), residues: 60 loop : -2.50 (0.41), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 77 TYR 0.012 0.001 TYR C 234 PHE 0.024 0.001 PHE D 256 TRP 0.069 0.006 TRP F 79 HIS 0.006 0.001 HIS D 75 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8364) covalent geometry : angle 1.02959 (11286) SS BOND : bond 0.00206 ( 18) SS BOND : angle 0.43067 ( 36) hydrogen bonds : bond 0.04605 ( 586) hydrogen bonds : angle 4.26064 ( 1740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1549.02 seconds wall clock time: 27 minutes 34.52 seconds (1654.52 seconds total)