Starting phenix.real_space_refine on Fri Aug 7 00:40:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qn9_53240/08_2026/9qn9_53240.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qn9_53240/08_2026/9qn9_53240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qn9_53240/08_2026/9qn9_53240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qn9_53240/08_2026/9qn9_53240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qn9_53240/08_2026/9qn9_53240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qn9_53240/08_2026/9qn9_53240.map" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 168 5.16 5 C 11952 2.51 5 N 2904 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18012 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "B" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "D" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "E" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "F" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "G" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "I" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "J" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "K" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "L" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Time building chain proxies: 3.81, per 1000 atoms: 0.21 Number of scatterers: 18012 At special positions: 0 Unit cell: (100.907, 94.3972, 160.801, 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 168 16.00 O 2988 8.00 N 2904 7.00 C 11952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 856.5 milliseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 71.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.621A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.609A pdb=" N VAL A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 105 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 128 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 41 removed outlier: 3.633A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.595A pdb=" N VAL B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 105 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 128 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 41 removed outlier: 3.621A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.619A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 105 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 128 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 41 removed outlier: 3.639A pdb=" N VAL D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.613A pdb=" N VAL D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 105 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 128 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 41 removed outlier: 3.640A pdb=" N VAL E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.597A pdb=" N VAL E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 105 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 128 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 41 removed outlier: 3.623A pdb=" N VAL F 27 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.616A pdb=" N VAL F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 105 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 128 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 23 through 41 removed outlier: 3.644A pdb=" N VAL G 27 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.598A pdb=" N VAL G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 105 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 128 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 23 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.640A pdb=" N VAL H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 removed outlier: 3.608A pdb=" N VAL H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 105 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 128 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 23 Processing helix chain 'I' and resid 23 through 41 removed outlier: 3.633A pdb=" N VAL I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.617A pdb=" N VAL I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 105 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 128 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 23 through 41 removed outlier: 3.658A pdb=" N VAL J 27 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 3.599A pdb=" N VAL J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 105 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 128 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 23 Processing helix chain 'K' and resid 23 through 41 removed outlier: 3.633A pdb=" N VAL K 27 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.595A pdb=" N VAL K 63 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 105 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 128 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 23 through 41 removed outlier: 3.575A pdb=" N VAL L 27 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.617A pdb=" N VAL L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 105 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 128 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.822A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.824A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.822A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.820A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.827A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.809A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.822A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.829A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.818A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.830A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.825A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.820A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5376 1.34 - 1.46: 4695 1.46 - 1.58: 8181 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 18492 Sorted by residual: bond pdb=" CA THR L 86 " pdb=" C THR L 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.79e-01 bond pdb=" CA THR J 86 " pdb=" C THR J 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.79e-01 bond pdb=" CA THR C 86 " pdb=" C THR C 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.72e-01 bond pdb=" CA THR D 86 " pdb=" C THR D 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.68e-01 bond pdb=" CA THR G 86 " pdb=" C THR G 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.57e-01 ... (remaining 18487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 24394 1.09 - 2.18: 596 2.18 - 3.26: 168 3.26 - 4.35: 42 4.35 - 5.44: 24 Bond angle restraints: 25224 Sorted by residual: angle pdb=" N ARG K 15 " pdb=" CA ARG K 15 " pdb=" CB ARG K 15 " ideal model delta sigma weight residual 113.65 110.31 3.34 1.47e+00 4.63e-01 5.16e+00 angle pdb=" N ARG B 15 " pdb=" CA ARG B 15 " pdb=" CB ARG B 15 " ideal model delta sigma weight residual 113.65 110.33 3.32 1.47e+00 4.63e-01 5.10e+00 angle pdb=" N ARG J 15 " pdb=" CA ARG J 15 " pdb=" CB ARG J 15 " ideal model delta sigma weight residual 113.65 110.35 3.30 1.47e+00 4.63e-01 5.03e+00 angle pdb=" N ARG C 15 " pdb=" CA ARG C 15 " pdb=" CB ARG C 15 " ideal model delta sigma weight residual 113.65 110.38 3.27 1.47e+00 4.63e-01 4.96e+00 angle pdb=" N ARG L 15 " pdb=" CA ARG L 15 " pdb=" CB ARG L 15 " ideal model delta sigma weight residual 113.65 110.38 3.27 1.47e+00 4.63e-01 4.95e+00 ... (remaining 25219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.32: 9614 12.32 - 24.64: 857 24.64 - 36.95: 213 36.95 - 49.27: 97 49.27 - 61.59: 19 Dihedral angle restraints: 10800 sinusoidal: 4128 harmonic: 6672 Sorted by residual: dihedral pdb=" SG CYS D 53 " pdb=" CB CYS D 179 " pdb=" SG CYS D 179 " pdb=" CA CYS D 179 " ideal model delta sinusoidal sigma weight residual -73.00 -11.41 -61.59 1 2.00e+01 2.50e-03 1.26e+01 dihedral pdb=" SG CYS K 53 " pdb=" CB CYS K 179 " pdb=" SG CYS K 179 " pdb=" CA CYS K 179 " ideal model delta sinusoidal sigma weight residual -73.00 -11.71 -61.29 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" SG CYS A 53 " pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " pdb=" CA CYS A 179 " ideal model delta sinusoidal sigma weight residual -73.00 -11.79 -61.21 1 2.00e+01 2.50e-03 1.24e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1638 0.023 - 0.047: 781 0.047 - 0.070: 398 0.070 - 0.093: 144 0.093 - 0.117: 63 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA THR F 86 " pdb=" N THR F 86 " pdb=" C THR F 86 " pdb=" CB THR F 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 3021 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 183 " -0.015 5.00e-02 4.00e+02 2.21e-02 7.80e-01 pdb=" N PRO K 184 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO K 184 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 184 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 183 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.98e-01 pdb=" N PRO F 184 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 183 " -0.012 5.00e-02 4.00e+02 1.86e-02 5.53e-01 pdb=" N PRO I 184 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.010 5.00e-02 4.00e+02 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 12811 3.09 - 3.54: 20650 3.54 - 3.99: 26497 3.99 - 4.45: 32718 4.45 - 4.90: 52119 Nonbonded interactions: 144795 Sorted by model distance: nonbonded pdb=" N ASN E 175 " pdb=" CG ASN E 175 " model vdw 2.636 2.680 nonbonded pdb=" N ASN I 175 " pdb=" CG ASN I 175 " model vdw 2.637 2.680 nonbonded pdb=" N ASN A 175 " pdb=" CG ASN A 175 " model vdw 2.637 2.680 nonbonded pdb=" N ASN D 175 " pdb=" CG ASN D 175 " model vdw 2.639 2.680 nonbonded pdb=" N ASN L 175 " pdb=" CG ASN L 175 " model vdw 2.649 2.680 ... (remaining 144790 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.840 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 15.870 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 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 0.019 18516 Z= 0.116 Angle : 0.479 5.438 25272 Z= 0.254 Chirality : 0.036 0.117 3024 Planarity : 0.003 0.024 3012 Dihedral : 10.746 58.481 6384 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.96 % Allowed : 4.49 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.70 (0.18), residues: 2208 helix: 3.97 (0.11), residues: 1488 sheet: 1.49 (0.49), residues: 132 loop : -1.73 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 164 TYR 0.005 0.001 TYR I 135 PHE 0.008 0.001 PHE C 51 TRP 0.005 0.001 TRP C 132 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (18492) covalent geometry : angle 0.47482 / 0.25 (25224) SS BOND : bond 0.00208 / 0.13 ( 24) SS BOND : angle 1.46362 / 0.92 ( 48) hydrogen bonds : bond 0.06407 / 4.37 ( 1320) hydrogen bonds : angle 3.28556 / 2.39 ( 3924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 374 time to evaluate : 0.446 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: A 10 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6001 (pp) REVERT: A 22 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8304 (ttm-80) REVERT: A 41 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 211 TYR cc_start: 0.8426 (t80) cc_final: 0.7924 (t80) REVERT: B 10 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6070 (pp) REVERT: B 41 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 211 TYR cc_start: 0.8424 (t80) cc_final: 0.7908 (t80) REVERT: C 10 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.5841 (pp) REVERT: C 22 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8288 (ttm-80) REVERT: C 41 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8244 (mm-30) REVERT: D 10 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5851 (pp) REVERT: D 22 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8293 (ttm-80) REVERT: D 41 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8228 (mm-30) REVERT: D 211 TYR cc_start: 0.8451 (t80) cc_final: 0.8009 (t80) REVERT: E 10 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5832 (pp) REVERT: E 22 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: E 41 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8311 (mm-30) REVERT: E 211 TYR cc_start: 0.8403 (t80) cc_final: 0.7841 (t80) REVERT: F 10 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5722 (pp) REVERT: F 22 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8325 (ttm-80) REVERT: F 41 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8241 (mm-30) REVERT: G 10 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5997 (pp) REVERT: G 22 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8308 (ttm-80) REVERT: G 41 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8268 (mm-30) REVERT: G 211 TYR cc_start: 0.8415 (t80) cc_final: 0.7831 (t80) REVERT: H 10 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5813 (pp) REVERT: H 22 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8383 (ttm-80) REVERT: H 211 TYR cc_start: 0.8361 (t80) cc_final: 0.7544 (t80) REVERT: I 10 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6297 (pp) REVERT: I 41 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8181 (mm-30) REVERT: I 211 TYR cc_start: 0.8396 (t80) cc_final: 0.8107 (t80) REVERT: J 10 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6017 (pp) REVERT: J 22 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8246 (ttm-80) REVERT: J 41 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8247 (mm-30) REVERT: K 10 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5829 (pp) REVERT: K 22 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8309 (ttm-80) REVERT: K 211 TYR cc_start: 0.8369 (t80) cc_final: 0.7906 (t80) REVERT: L 10 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5781 (pp) REVERT: L 22 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8276 (ttm-80) REVERT: L 41 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8224 (mm-30) outliers start: 60 outliers final: 17 residues processed: 414 average time/residue: 0.1193 time to fit residues: 74.1807 Evaluate side-chains 314 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 175 ASN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.121823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.085853 restraints weight = 23604.473| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.81 r_work: 0.2837 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18516 Z= 0.151 Angle : 0.514 5.450 25272 Z= 0.254 Chirality : 0.039 0.125 3024 Planarity : 0.003 0.029 3012 Dihedral : 5.666 53.399 2470 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.66 % Allowed : 9.86 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.98 (0.18), residues: 2208 helix: 4.18 (0.11), residues: 1488 sheet: 1.92 (0.49), residues: 132 loop : -1.71 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 183 TYR 0.008 0.001 TYR L 65 PHE 0.011 0.001 PHE C 68 TRP 0.005 0.001 TRP J 132 HIS 0.005 0.001 HIS K 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.15 (18492) covalent geometry : angle 0.51069 / 0.25 (25224) SS BOND : bond 0.00326 / 0.21 ( 24) SS BOND : angle 1.37628 / 0.86 ( 48) hydrogen bonds : bond 0.03653 / 2.51 ( 1320) hydrogen bonds : angle 2.84315 / 2.08 ( 3924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.494 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: A 10 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6020 (pp) REVERT: A 22 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8289 (ttm-80) REVERT: A 41 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 211 TYR cc_start: 0.8458 (t80) cc_final: 0.7949 (t80) REVERT: B 10 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5929 (pp) REVERT: B 22 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: B 41 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 211 TYR cc_start: 0.8481 (t80) cc_final: 0.7985 (t80) REVERT: C 10 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5791 (pp) REVERT: C 22 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8318 (ttm-80) REVERT: C 41 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 211 TYR cc_start: 0.8309 (t80) cc_final: 0.7939 (t80) REVERT: D 10 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5888 (pp) REVERT: D 22 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8298 (ttm-80) REVERT: D 41 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 211 TYR cc_start: 0.8472 (t80) cc_final: 0.8027 (t80) REVERT: E 10 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5814 (pp) REVERT: E 22 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8282 (ttm-80) REVERT: E 41 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8293 (mm-30) REVERT: E 211 TYR cc_start: 0.8437 (t80) cc_final: 0.7856 (t80) REVERT: F 10 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5761 (pp) REVERT: F 22 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8338 (ttm-80) REVERT: F 41 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8227 (mm-30) REVERT: F 211 TYR cc_start: 0.8278 (t80) cc_final: 0.7902 (t80) REVERT: G 10 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.5894 (pp) REVERT: G 22 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8270 (ttm-80) REVERT: G 41 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8258 (mm-30) REVERT: G 211 TYR cc_start: 0.8460 (t80) cc_final: 0.7854 (t80) REVERT: H 10 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5781 (pp) REVERT: H 22 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8355 (ttm-80) REVERT: H 211 TYR cc_start: 0.8340 (t80) cc_final: 0.7589 (t80) REVERT: I 10 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6206 (pp) REVERT: I 41 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8210 (mm-30) REVERT: I 211 TYR cc_start: 0.8446 (t80) cc_final: 0.8146 (t80) REVERT: J 10 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5979 (pp) REVERT: J 22 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8239 (ttm-80) REVERT: J 41 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8279 (mm-30) REVERT: K 10 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5791 (pp) REVERT: K 22 ARG cc_start: 0.8507 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: K 41 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8282 (mm-30) REVERT: K 211 TYR cc_start: 0.8437 (t80) cc_final: 0.7962 (t80) REVERT: L 10 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5756 (pp) REVERT: L 22 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8211 (ttm-80) REVERT: L 41 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8229 (mm-30) outliers start: 54 outliers final: 40 residues processed: 305 average time/residue: 0.1193 time to fit residues: 54.1971 Evaluate side-chains 311 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 158 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 202 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 195 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 14 ASN ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087866 restraints weight = 23899.463| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.81 r_work: 0.2878 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18516 Z= 0.092 Angle : 0.446 5.296 25272 Z= 0.220 Chirality : 0.037 0.121 3024 Planarity : 0.003 0.021 3012 Dihedral : 5.739 59.020 2470 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.47 % Allowed : 13.95 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.22 (0.18), residues: 2208 helix: 4.38 (0.11), residues: 1488 sheet: 1.88 (0.49), residues: 132 loop : -1.64 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 22 TYR 0.005 0.001 TYR G 135 PHE 0.009 0.001 PHE F 51 TRP 0.005 0.001 TRP J 132 HIS 0.002 0.000 HIS E 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (18492) covalent geometry : angle 0.44384 / 0.22 (25224) SS BOND : bond 0.00182 / 0.12 ( 24) SS BOND : angle 1.17875 / 0.73 ( 48) hydrogen bonds : bond 0.03227 / 2.21 ( 1320) hydrogen bonds : angle 2.70954 / 1.98 ( 3924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.479 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: A 10 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6013 (pp) REVERT: A 22 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8300 (ttm-80) REVERT: A 41 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8201 (mm-30) REVERT: A 211 TYR cc_start: 0.8483 (t80) cc_final: 0.7942 (t80) REVERT: B 10 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.5915 (pp) REVERT: B 22 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: B 41 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 211 TYR cc_start: 0.8478 (t80) cc_final: 0.7950 (t80) REVERT: C 10 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5777 (pp) REVERT: C 22 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8311 (ttm-80) REVERT: C 41 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 65 TYR cc_start: 0.9140 (t80) cc_final: 0.8923 (t80) REVERT: C 211 TYR cc_start: 0.8349 (t80) cc_final: 0.7916 (t80) REVERT: D 10 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.5948 (pp) REVERT: D 22 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8316 (ttm-80) REVERT: D 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8174 (mm-30) REVERT: D 211 TYR cc_start: 0.8483 (t80) cc_final: 0.8016 (t80) REVERT: E 10 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5798 (pp) REVERT: E 22 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8279 (ttm-80) REVERT: E 41 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8266 (mm-30) REVERT: E 211 TYR cc_start: 0.8453 (t80) cc_final: 0.7891 (t80) REVERT: F 10 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5761 (pp) REVERT: F 22 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: F 41 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8191 (mm-30) REVERT: F 65 TYR cc_start: 0.9142 (t80) cc_final: 0.8921 (t80) REVERT: F 105 MET cc_start: 0.3426 (mmp) cc_final: 0.3216 (mmm) REVERT: F 211 TYR cc_start: 0.8317 (t80) cc_final: 0.7950 (t80) REVERT: G 10 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6050 (pp) REVERT: G 22 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8285 (ttm-80) REVERT: G 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8214 (mm-30) REVERT: G 211 TYR cc_start: 0.8465 (t80) cc_final: 0.7895 (t80) REVERT: H 10 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5774 (pp) REVERT: H 22 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8360 (ttm-80) REVERT: H 211 TYR cc_start: 0.8345 (t80) cc_final: 0.7569 (t80) REVERT: I 10 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6301 (pp) REVERT: I 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8164 (mm-30) REVERT: I 65 TYR cc_start: 0.9156 (t80) cc_final: 0.8936 (t80) REVERT: I 211 TYR cc_start: 0.8454 (t80) cc_final: 0.8153 (t80) REVERT: J 10 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6012 (pp) REVERT: J 22 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: J 41 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8279 (mm-30) REVERT: K 10 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5860 (pp) REVERT: K 41 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8273 (mm-30) REVERT: K 211 TYR cc_start: 0.8452 (t80) cc_final: 0.7938 (t80) REVERT: L 10 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5774 (pp) REVERT: L 22 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8220 (ttm-80) REVERT: L 41 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8151 (mm-30) outliers start: 50 outliers final: 28 residues processed: 299 average time/residue: 0.1236 time to fit residues: 55.1276 Evaluate side-chains 304 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 175 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 85 optimal weight: 8.9990 chunk 126 optimal weight: 30.0000 chunk 206 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 120 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 58.2358 > 50:) chunk 118 optimal weight: 0.9990 chunk 180 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 57 GLN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 GLN J 97 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 97 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.082593 restraints weight = 24156.531| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 1.85 r_work: 0.2805 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 18516 Z= 0.220 Angle : 0.530 5.673 25272 Z= 0.263 Chirality : 0.041 0.135 3024 Planarity : 0.004 0.037 3012 Dihedral : 5.597 55.163 2466 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 3.45 % Allowed : 14.94 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 3.93 (0.18), residues: 2208 helix: 4.08 (0.11), residues: 1500 sheet: 1.98 (0.49), residues: 132 loop : -1.67 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG I 22 TYR 0.010 0.001 TYR L 65 PHE 0.015 0.002 PHE J 68 TRP 0.005 0.001 TRP C 44 HIS 0.006 0.001 HIS J 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.22 (18492) covalent geometry : angle 0.52598 / 0.26 (25224) SS BOND : bond 0.00466 / 0.29 ( 24) SS BOND : angle 1.53396 / 0.96 ( 48) hydrogen bonds : bond 0.03954 / 2.73 ( 1320) hydrogen bonds : angle 2.84500 / 2.08 ( 3924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 250 time to evaluate : 0.564 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: A 10 LEU cc_start: 0.6431 (OUTLIER) cc_final: 0.5943 (pp) REVERT: A 22 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8306 (ttm-80) REVERT: A 41 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 211 TYR cc_start: 0.8448 (t80) cc_final: 0.7933 (t80) REVERT: B 10 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5813 (pp) REVERT: B 22 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.8003 (ttm-80) REVERT: B 41 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 211 TYR cc_start: 0.8500 (t80) cc_final: 0.7995 (t80) REVERT: C 10 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5730 (pp) REVERT: C 22 ARG cc_start: 0.8508 (ttm-80) cc_final: 0.8300 (ttm-80) REVERT: C 41 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8235 (mm-30) REVERT: C 211 TYR cc_start: 0.8329 (t80) cc_final: 0.7904 (t80) REVERT: D 10 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5661 (pp) REVERT: D 22 ARG cc_start: 0.8542 (ttm-80) cc_final: 0.8320 (ttm-80) REVERT: D 41 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8221 (mm-30) REVERT: D 211 TYR cc_start: 0.8471 (t80) cc_final: 0.8019 (t80) REVERT: E 10 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5796 (pp) REVERT: E 22 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8344 (ttm-80) REVERT: E 41 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8246 (mm-30) REVERT: E 211 TYR cc_start: 0.8460 (t80) cc_final: 0.7886 (t80) REVERT: F 10 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5724 (pp) REVERT: F 41 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8223 (mm-30) REVERT: F 211 TYR cc_start: 0.8332 (t80) cc_final: 0.7963 (t80) REVERT: G 10 LEU cc_start: 0.6538 (OUTLIER) cc_final: 0.6009 (pp) REVERT: G 41 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8230 (mm-30) REVERT: G 211 TYR cc_start: 0.8459 (t80) cc_final: 0.7900 (t80) REVERT: H 10 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5654 (pp) REVERT: H 22 ARG cc_start: 0.8598 (ttm-80) cc_final: 0.8382 (ttm-80) REVERT: H 41 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8263 (mm-30) REVERT: H 211 TYR cc_start: 0.8334 (t80) cc_final: 0.7634 (t80) REVERT: I 10 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.5998 (pp) REVERT: I 41 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8172 (mm-30) REVERT: I 211 TYR cc_start: 0.8449 (t80) cc_final: 0.8182 (t80) REVERT: J 10 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.5867 (pp) REVERT: J 22 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8266 (ttm-80) REVERT: J 41 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8265 (mm-30) REVERT: K 10 LEU cc_start: 0.6224 (OUTLIER) cc_final: 0.5737 (pp) REVERT: K 41 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8271 (mm-30) REVERT: K 211 TYR cc_start: 0.8442 (t80) cc_final: 0.7929 (t80) REVERT: L 10 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5648 (pp) REVERT: L 22 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8184 (ttm-80) REVERT: L 41 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8219 (mm-30) outliers start: 70 outliers final: 41 residues processed: 314 average time/residue: 0.1258 time to fit residues: 58.9043 Evaluate side-chains 300 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 247 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 26 SER Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain F residue 210 VAL Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 175 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 29 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 162 optimal weight: 30.0000 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 6.9990 chunk 63 optimal weight: 0.0050 chunk 156 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086100 restraints weight = 23924.110| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.80 r_work: 0.2851 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18516 Z= 0.102 Angle : 0.454 6.458 25272 Z= 0.225 Chirality : 0.038 0.123 3024 Planarity : 0.003 0.021 3012 Dihedral : 5.441 50.229 2464 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.63 % Allowed : 18.39 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.17 (0.18), residues: 2208 helix: 4.24 (0.11), residues: 1500 sheet: 2.19 (0.51), residues: 132 loop : -1.56 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 22 TYR 0.005 0.001 TYR D 65 PHE 0.010 0.001 PHE F 51 TRP 0.006 0.001 TRP J 132 HIS 0.002 0.000 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (18492) covalent geometry : angle 0.45207 / 0.22 (25224) SS BOND : bond 0.00199 / 0.13 ( 24) SS BOND : angle 1.13709 / 0.71 ( 48) hydrogen bonds : bond 0.03287 / 2.25 ( 1320) hydrogen bonds : angle 2.68999 / 1.97 ( 3924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.500 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: A 10 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5994 (pp) REVERT: A 22 ARG cc_start: 0.8500 (ttm-80) cc_final: 0.8291 (ttm-80) REVERT: A 41 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 211 TYR cc_start: 0.8471 (t80) cc_final: 0.7986 (t80) REVERT: B 10 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.5827 (pp) REVERT: B 22 ARG cc_start: 0.8393 (ttm-80) cc_final: 0.7987 (ttm-80) REVERT: B 41 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 211 TYR cc_start: 0.8504 (t80) cc_final: 0.7968 (t80) REVERT: C 10 LEU cc_start: 0.6202 (OUTLIER) cc_final: 0.5711 (pp) REVERT: C 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8033 (tp30) REVERT: C 211 TYR cc_start: 0.8326 (t80) cc_final: 0.7842 (t80) REVERT: D 10 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5780 (pp) REVERT: D 22 ARG cc_start: 0.8549 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: D 41 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8219 (mm-30) REVERT: D 211 TYR cc_start: 0.8510 (t80) cc_final: 0.8035 (t80) REVERT: E 10 LEU cc_start: 0.6245 (OUTLIER) cc_final: 0.5743 (pp) REVERT: E 22 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: E 41 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8246 (mm-30) REVERT: E 211 TYR cc_start: 0.8455 (t80) cc_final: 0.7844 (t80) REVERT: F 10 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5731 (pp) REVERT: F 41 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8037 (tp30) REVERT: F 211 TYR cc_start: 0.8318 (t80) cc_final: 0.7889 (t80) REVERT: G 10 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.6090 (pp) REVERT: G 41 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8239 (mm-30) REVERT: G 211 TYR cc_start: 0.8478 (t80) cc_final: 0.7955 (t80) REVERT: H 10 LEU cc_start: 0.6098 (OUTLIER) cc_final: 0.5686 (pp) REVERT: H 22 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8371 (ttm-80) REVERT: H 41 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8285 (mm-30) REVERT: H 211 TYR cc_start: 0.8349 (t80) cc_final: 0.7595 (t80) REVERT: I 10 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5986 (pp) REVERT: I 41 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8144 (mm-30) REVERT: I 211 TYR cc_start: 0.8460 (t80) cc_final: 0.8146 (t80) REVERT: J 10 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.5931 (pp) REVERT: J 22 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8291 (ttm-80) REVERT: J 41 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8295 (mm-30) REVERT: K 10 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5753 (pp) REVERT: K 41 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8298 (mm-30) REVERT: K 211 TYR cc_start: 0.8406 (t80) cc_final: 0.7901 (t80) REVERT: L 10 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5661 (pp) REVERT: L 22 ARG cc_start: 0.8561 (ttm-80) cc_final: 0.8209 (ttm-80) REVERT: L 41 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8062 (tp30) outliers start: 33 outliers final: 18 residues processed: 280 average time/residue: 0.1312 time to fit residues: 54.5675 Evaluate side-chains 277 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 247 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 113 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 169 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 203 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 210 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 14 ASN ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.122719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.086698 restraints weight = 23749.599| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.83 r_work: 0.2862 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18516 Z= 0.098 Angle : 0.445 5.789 25272 Z= 0.219 Chirality : 0.038 0.119 3024 Planarity : 0.002 0.022 3012 Dihedral : 5.277 51.261 2460 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.12 % Allowed : 19.18 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.27 (0.18), residues: 2208 helix: 4.33 (0.11), residues: 1500 sheet: 2.25 (0.51), residues: 132 loop : -1.57 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 22 TYR 0.004 0.001 TYR F 65 PHE 0.012 0.001 PHE I 68 TRP 0.006 0.001 TRP E 132 HIS 0.003 0.001 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (18492) covalent geometry : angle 0.44218 / 0.22 (25224) SS BOND : bond 0.00189 / 0.12 ( 24) SS BOND : angle 1.13285 / 0.71 ( 48) hydrogen bonds : bond 0.03138 / 2.15 ( 1320) hydrogen bonds : angle 2.62909 / 1.92 ( 3924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 265 time to evaluate : 0.532 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: A 10 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6021 (pp) REVERT: A 41 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 211 TYR cc_start: 0.8472 (t80) cc_final: 0.7982 (t80) REVERT: B 10 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.5944 (pp) REVERT: B 41 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8228 (mm-30) REVERT: B 211 TYR cc_start: 0.8489 (t80) cc_final: 0.7910 (t80) REVERT: C 10 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5882 (pp) REVERT: C 41 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8065 (tp30) REVERT: C 211 TYR cc_start: 0.8333 (t80) cc_final: 0.7795 (t80) REVERT: D 10 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5699 (pp) REVERT: D 41 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8241 (mm-30) REVERT: D 211 TYR cc_start: 0.8501 (t80) cc_final: 0.8039 (t80) REVERT: E 10 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5589 (pp) REVERT: E 22 ARG cc_start: 0.8489 (ttm-80) cc_final: 0.8278 (ttm-80) REVERT: E 41 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8230 (mm-30) REVERT: E 211 TYR cc_start: 0.8457 (t80) cc_final: 0.7854 (t80) REVERT: F 10 LEU cc_start: 0.6172 (OUTLIER) cc_final: 0.5722 (pp) REVERT: F 41 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8042 (tp30) REVERT: F 167 LYS cc_start: 0.9347 (mmtp) cc_final: 0.9123 (mmtt) REVERT: F 211 TYR cc_start: 0.8328 (t80) cc_final: 0.7841 (t80) REVERT: G 10 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6071 (pp) REVERT: G 22 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8242 (ttm-80) REVERT: G 41 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8096 (tp30) REVERT: G 211 TYR cc_start: 0.8462 (t80) cc_final: 0.7947 (t80) REVERT: H 10 LEU cc_start: 0.6106 (OUTLIER) cc_final: 0.5685 (pp) REVERT: H 22 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8341 (ttm-80) REVERT: H 41 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8307 (mm-30) REVERT: H 211 TYR cc_start: 0.8353 (t80) cc_final: 0.7593 (t80) REVERT: I 10 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5951 (pp) REVERT: I 41 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8161 (mm-30) REVERT: I 211 TYR cc_start: 0.8453 (t80) cc_final: 0.8110 (t80) REVERT: J 10 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5778 (pp) REVERT: J 41 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8220 (tp30) REVERT: J 211 TYR cc_start: 0.8411 (t80) cc_final: 0.7710 (t80) REVERT: K 10 LEU cc_start: 0.6284 (OUTLIER) cc_final: 0.5818 (pp) REVERT: K 41 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8301 (mm-30) REVERT: K 211 TYR cc_start: 0.8415 (t80) cc_final: 0.7877 (t80) REVERT: L 10 LEU cc_start: 0.6063 (OUTLIER) cc_final: 0.5669 (pp) REVERT: L 22 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8195 (ttm-80) REVERT: L 41 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8055 (tp30) outliers start: 43 outliers final: 23 residues processed: 300 average time/residue: 0.1362 time to fit residues: 60.5533 Evaluate side-chains 292 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 257 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 175 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 35 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.0010 chunk 28 optimal weight: 8.9990 chunk 90 optimal weight: 30.0000 chunk 157 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 HIS ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 HIS L 14 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088202 restraints weight = 23864.438| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.80 r_work: 0.2883 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18516 Z= 0.091 Angle : 0.439 6.600 25272 Z= 0.217 Chirality : 0.038 0.122 3024 Planarity : 0.002 0.018 3012 Dihedral : 5.271 51.748 2460 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.97 % Allowed : 19.67 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.37 (0.18), residues: 2208 helix: 4.40 (0.11), residues: 1500 sheet: 2.29 (0.51), residues: 132 loop : -1.52 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 22 TYR 0.003 0.000 TYR E 65 PHE 0.009 0.001 PHE F 68 TRP 0.005 0.001 TRP C 132 HIS 0.002 0.000 HIS H 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 (18492) covalent geometry : angle 0.43704 / 0.22 (25224) SS BOND : bond 0.00162 / 0.10 ( 24) SS BOND : angle 1.06969 / 0.67 ( 48) hydrogen bonds : bond 0.02970 / 2.03 ( 1320) hydrogen bonds : angle 2.59443 / 1.90 ( 3924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 0.651 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: A 10 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5962 (pp) REVERT: A 41 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8196 (mm-30) REVERT: A 211 TYR cc_start: 0.8484 (t80) cc_final: 0.7949 (t80) REVERT: B 10 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5914 (pp) REVERT: B 41 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 211 TYR cc_start: 0.8486 (t80) cc_final: 0.7916 (t80) REVERT: C 10 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5842 (pp) REVERT: C 41 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8063 (tp30) REVERT: C 65 TYR cc_start: 0.9088 (t80) cc_final: 0.8798 (t80) REVERT: C 211 TYR cc_start: 0.8353 (t80) cc_final: 0.7829 (t80) REVERT: D 10 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5801 (pp) REVERT: D 41 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8210 (mm-30) REVERT: D 211 TYR cc_start: 0.8502 (t80) cc_final: 0.8048 (t80) REVERT: E 10 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5686 (pp) REVERT: E 22 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: E 41 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8236 (mm-30) REVERT: E 211 TYR cc_start: 0.8465 (t80) cc_final: 0.7881 (t80) REVERT: F 10 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5808 (pp) REVERT: F 41 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8030 (tp30) REVERT: F 65 TYR cc_start: 0.9063 (t80) cc_final: 0.8755 (t80) REVERT: F 211 TYR cc_start: 0.8334 (t80) cc_final: 0.7790 (t80) REVERT: G 10 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6054 (pp) REVERT: G 22 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8236 (ttm-80) REVERT: G 41 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8087 (tp30) REVERT: G 211 TYR cc_start: 0.8468 (t80) cc_final: 0.7908 (t80) REVERT: H 10 LEU cc_start: 0.6129 (OUTLIER) cc_final: 0.5718 (pp) REVERT: H 41 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8301 (mm-30) REVERT: H 211 TYR cc_start: 0.8372 (t80) cc_final: 0.7570 (t80) REVERT: I 10 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.5978 (pp) REVERT: I 41 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8110 (mm-30) REVERT: I 211 TYR cc_start: 0.8458 (t80) cc_final: 0.8075 (t80) REVERT: J 10 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5785 (pp) REVERT: J 41 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8200 (tp30) REVERT: J 211 TYR cc_start: 0.8424 (t80) cc_final: 0.7687 (t80) REVERT: K 10 LEU cc_start: 0.6272 (OUTLIER) cc_final: 0.5858 (pp) REVERT: K 41 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8282 (mm-30) REVERT: K 211 TYR cc_start: 0.8432 (t80) cc_final: 0.7897 (t80) REVERT: L 10 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5810 (pp) REVERT: L 22 ARG cc_start: 0.8530 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: L 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8048 (tp30) outliers start: 40 outliers final: 21 residues processed: 313 average time/residue: 0.1220 time to fit residues: 57.1554 Evaluate side-chains 306 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 273 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 175 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 167 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 166 optimal weight: 3.9990 chunk 152 optimal weight: 1.9990 chunk 133 optimal weight: 0.4980 chunk 80 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 HIS ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087051 restraints weight = 23805.854| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.87 r_work: 0.2873 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18516 Z= 0.110 Angle : 0.465 6.291 25272 Z= 0.229 Chirality : 0.038 0.126 3024 Planarity : 0.002 0.022 3012 Dihedral : 5.280 51.392 2460 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.87 % Allowed : 20.02 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.36 (0.18), residues: 2208 helix: 4.38 (0.11), residues: 1500 sheet: 2.34 (0.51), residues: 132 loop : -1.52 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 22 TYR 0.008 0.001 TYR L 135 PHE 0.012 0.001 PHE H 68 TRP 0.005 0.001 TRP C 24 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (18492) covalent geometry : angle 0.46227 / 0.23 (25224) SS BOND : bond 0.00237 / 0.15 ( 24) SS BOND : angle 1.18030 / 0.74 ( 48) hydrogen bonds : bond 0.03107 / 2.13 ( 1320) hydrogen bonds : angle 2.60964 / 1.91 ( 3924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 263 time to evaluate : 0.775 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: A 10 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5789 (pp) REVERT: A 41 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8174 (mm-30) REVERT: A 211 TYR cc_start: 0.8443 (t80) cc_final: 0.7908 (t80) REVERT: B 10 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5940 (pp) REVERT: B 41 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8190 (mm-30) REVERT: B 211 TYR cc_start: 0.8463 (t80) cc_final: 0.7895 (t80) REVERT: C 10 LEU cc_start: 0.6253 (OUTLIER) cc_final: 0.5839 (pp) REVERT: C 41 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8046 (tp30) REVERT: C 211 TYR cc_start: 0.8321 (t80) cc_final: 0.7746 (t80) REVERT: D 10 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5736 (pp) REVERT: D 41 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8196 (mm-30) REVERT: D 211 TYR cc_start: 0.8447 (t80) cc_final: 0.7991 (t80) REVERT: E 10 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5680 (pp) REVERT: E 41 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8201 (mm-30) REVERT: E 211 TYR cc_start: 0.8443 (t80) cc_final: 0.7864 (t80) REVERT: F 10 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5733 (pp) REVERT: F 41 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8017 (tp30) REVERT: F 211 TYR cc_start: 0.8314 (t80) cc_final: 0.7779 (t80) REVERT: G 10 LEU cc_start: 0.6501 (OUTLIER) cc_final: 0.6053 (pp) REVERT: G 22 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8284 (ttm-80) REVERT: G 41 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8067 (tp30) REVERT: G 211 TYR cc_start: 0.8446 (t80) cc_final: 0.7885 (t80) REVERT: H 10 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5719 (pp) REVERT: H 41 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8303 (mm-30) REVERT: H 211 TYR cc_start: 0.8352 (t80) cc_final: 0.7557 (t80) REVERT: I 10 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5982 (pp) REVERT: I 41 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8132 (mm-30) REVERT: I 211 TYR cc_start: 0.8464 (t80) cc_final: 0.8084 (t80) REVERT: J 10 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5715 (pp) REVERT: J 211 TYR cc_start: 0.8394 (t80) cc_final: 0.7654 (t80) REVERT: K 10 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5688 (pp) REVERT: K 41 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8247 (mm-30) REVERT: K 211 TYR cc_start: 0.8422 (t80) cc_final: 0.7850 (t80) REVERT: L 10 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5766 (pp) REVERT: L 41 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8011 (tp30) outliers start: 38 outliers final: 23 residues processed: 290 average time/residue: 0.1545 time to fit residues: 66.4833 Evaluate side-chains 297 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 106 optimal weight: 0.9980 chunk 110 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 115 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 90 optimal weight: 30.0000 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 HIS ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085042 restraints weight = 23925.762| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 1.85 r_work: 0.2838 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18516 Z= 0.166 Angle : 0.511 7.378 25272 Z= 0.254 Chirality : 0.040 0.133 3024 Planarity : 0.003 0.028 3012 Dihedral : 5.328 50.621 2460 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.73 % Allowed : 20.17 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.22 (0.18), residues: 2208 helix: 4.28 (0.11), residues: 1500 sheet: 2.23 (0.50), residues: 132 loop : -1.55 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 22 TYR 0.011 0.001 TYR H 65 PHE 0.014 0.002 PHE F 68 TRP 0.006 0.001 TRP J 24 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.17 (18492) covalent geometry : angle 0.50783 / 0.25 (25224) SS BOND : bond 0.00370 / 0.23 ( 24) SS BOND : angle 1.36342 / 0.85 ( 48) hydrogen bonds : bond 0.03450 / 2.37 ( 1320) hydrogen bonds : angle 2.68325 / 1.97 ( 3924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.687 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: A 10 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5733 (pp) REVERT: A 41 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8208 (mm-30) REVERT: A 211 TYR cc_start: 0.8429 (t80) cc_final: 0.7934 (t80) REVERT: B 10 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5918 (pp) REVERT: B 41 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8178 (mm-30) REVERT: B 167 LYS cc_start: 0.9366 (mmtm) cc_final: 0.9090 (mmmt) REVERT: B 211 TYR cc_start: 0.8454 (t80) cc_final: 0.7874 (t80) REVERT: C 10 LEU cc_start: 0.6162 (OUTLIER) cc_final: 0.5787 (pp) REVERT: C 41 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8034 (tp30) REVERT: C 211 TYR cc_start: 0.8315 (t80) cc_final: 0.7800 (t80) REVERT: D 10 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5771 (pp) REVERT: D 41 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8209 (mm-30) REVERT: D 211 TYR cc_start: 0.8446 (t80) cc_final: 0.7985 (t80) REVERT: E 10 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5666 (pp) REVERT: E 41 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8214 (mm-30) REVERT: E 211 TYR cc_start: 0.8419 (t80) cc_final: 0.7835 (t80) REVERT: F 10 LEU cc_start: 0.5995 (OUTLIER) cc_final: 0.5604 (pp) REVERT: F 41 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8019 (tp30) REVERT: F 211 TYR cc_start: 0.8322 (t80) cc_final: 0.7791 (t80) REVERT: G 10 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5995 (pp) REVERT: G 22 ARG cc_start: 0.8498 (ttm-80) cc_final: 0.8274 (ttm-80) REVERT: G 41 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8052 (tp30) REVERT: G 211 TYR cc_start: 0.8434 (t80) cc_final: 0.7916 (t80) REVERT: H 10 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5736 (pp) REVERT: H 41 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8314 (mm-30) REVERT: H 211 TYR cc_start: 0.8342 (t80) cc_final: 0.7542 (t80) REVERT: I 10 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5970 (pp) REVERT: I 41 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8162 (mm-30) REVERT: I 167 LYS cc_start: 0.9348 (mmtp) cc_final: 0.9118 (mmtt) REVERT: I 211 TYR cc_start: 0.8453 (t80) cc_final: 0.8114 (t80) REVERT: J 10 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5724 (pp) REVERT: J 211 TYR cc_start: 0.8380 (t80) cc_final: 0.7678 (t80) REVERT: K 10 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5712 (pp) REVERT: K 41 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8268 (mm-30) REVERT: K 211 TYR cc_start: 0.8417 (t80) cc_final: 0.7887 (t80) REVERT: L 10 LEU cc_start: 0.5929 (OUTLIER) cc_final: 0.5596 (pp) REVERT: L 22 ARG cc_start: 0.8444 (ttm-80) cc_final: 0.8183 (ttm-80) REVERT: L 41 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8032 (tp30) REVERT: L 167 LYS cc_start: 0.9339 (mmtp) cc_final: 0.9106 (mmtt) outliers start: 35 outliers final: 22 residues processed: 280 average time/residue: 0.1604 time to fit residues: 65.9754 Evaluate side-chains 282 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 248 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 124 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 0.0870 chunk 27 optimal weight: 3.9990 chunk 206 optimal weight: 10.0000 chunk 178 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.123753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087149 restraints weight = 23630.352| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.86 r_work: 0.2874 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.068 18516 Z= 0.103 Angle : 0.472 7.162 25272 Z= 0.235 Chirality : 0.038 0.129 3024 Planarity : 0.003 0.023 3012 Dihedral : 5.337 51.549 2460 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 1.73 % Allowed : 20.12 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.38 (0.18), residues: 2208 helix: 4.39 (0.11), residues: 1500 sheet: 2.35 (0.51), residues: 132 loop : -1.49 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 22 TYR 0.009 0.001 TYR H 65 PHE 0.010 0.001 PHE F 68 TRP 0.005 0.001 TRP C 132 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.10 (18492) covalent geometry : angle 0.47034 / 0.23 (25224) SS BOND : bond 0.00179 / 0.11 ( 24) SS BOND : angle 1.13525 / 0.71 ( 48) hydrogen bonds : bond 0.03125 / 2.14 ( 1320) hydrogen bonds : angle 2.62803 / 1.93 ( 3924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 265 time to evaluate : 0.758 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: A 10 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5701 (pp) REVERT: A 41 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 211 TYR cc_start: 0.8456 (t80) cc_final: 0.7921 (t80) REVERT: B 10 LEU cc_start: 0.6269 (OUTLIER) cc_final: 0.5861 (pp) REVERT: B 41 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8190 (mm-30) REVERT: B 167 LYS cc_start: 0.9362 (mmtm) cc_final: 0.9117 (mmtt) REVERT: B 211 TYR cc_start: 0.8469 (t80) cc_final: 0.7895 (t80) REVERT: C 10 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5795 (pp) REVERT: C 41 GLU cc_start: 0.8510 (mm-30) cc_final: 0.8044 (tp30) REVERT: C 211 TYR cc_start: 0.8328 (t80) cc_final: 0.7762 (t80) REVERT: D 10 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5751 (pp) REVERT: D 41 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8224 (mm-30) REVERT: D 211 TYR cc_start: 0.8449 (t80) cc_final: 0.7945 (t80) REVERT: E 10 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5713 (pp) REVERT: E 22 ARG cc_start: 0.8563 (ttp-170) cc_final: 0.8350 (ttm-80) REVERT: E 41 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8218 (mm-30) REVERT: E 211 TYR cc_start: 0.8443 (t80) cc_final: 0.7867 (t80) REVERT: F 10 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5732 (pp) REVERT: F 41 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8023 (tp30) REVERT: F 211 TYR cc_start: 0.8326 (t80) cc_final: 0.7805 (t80) REVERT: G 10 LEU cc_start: 0.6429 (OUTLIER) cc_final: 0.6015 (pp) REVERT: G 22 ARG cc_start: 0.8487 (ttm-80) cc_final: 0.8162 (ttm-80) REVERT: G 41 GLU cc_start: 0.8541 (mm-30) cc_final: 0.8065 (tp30) REVERT: G 211 TYR cc_start: 0.8444 (t80) cc_final: 0.7892 (t80) REVERT: H 10 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5698 (pp) REVERT: H 41 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8304 (mm-30) REVERT: H 211 TYR cc_start: 0.8354 (t80) cc_final: 0.7560 (t80) REVERT: I 10 LEU cc_start: 0.6400 (OUTLIER) cc_final: 0.6049 (pp) REVERT: I 41 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8107 (mm-30) REVERT: I 167 LYS cc_start: 0.9327 (mmtp) cc_final: 0.9094 (mmtt) REVERT: I 211 TYR cc_start: 0.8468 (t80) cc_final: 0.8093 (t80) REVERT: J 10 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5746 (pp) REVERT: J 211 TYR cc_start: 0.8389 (t80) cc_final: 0.7649 (t80) REVERT: K 10 LEU cc_start: 0.6064 (OUTLIER) cc_final: 0.5719 (pp) REVERT: K 41 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8261 (mm-30) REVERT: K 211 TYR cc_start: 0.8430 (t80) cc_final: 0.7861 (t80) REVERT: L 10 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5806 (pp) REVERT: L 22 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8179 (ttm-80) REVERT: L 41 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8015 (tp30) REVERT: L 167 LYS cc_start: 0.9317 (mmtp) cc_final: 0.9082 (mmtt) outliers start: 35 outliers final: 21 residues processed: 290 average time/residue: 0.1614 time to fit residues: 68.9337 Evaluate side-chains 295 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 262 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 105 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 97 HIS Chi-restraints excluded: chain B residue 217 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 85 SER Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 149 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 190 optimal weight: 5.9990 chunk 131 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 97 HIS ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.087392 restraints weight = 23776.315| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.88 r_work: 0.2877 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 18516 Z= 0.102 Angle : 0.468 6.996 25272 Z= 0.232 Chirality : 0.038 0.124 3024 Planarity : 0.002 0.021 3012 Dihedral : 5.332 51.821 2460 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.68 % Allowed : 20.51 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 4.40 (0.18), residues: 2208 helix: 4.41 (0.11), residues: 1500 sheet: 2.34 (0.51), residues: 132 loop : -1.48 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 22 TYR 0.009 0.001 TYR H 65 PHE 0.010 0.001 PHE F 68 TRP 0.005 0.001 TRP C 132 HIS 0.005 0.001 HIS A 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.10 (18492) covalent geometry : angle 0.46556 / 0.23 (25224) SS BOND : bond 0.00184 / 0.12 ( 24) SS BOND : angle 1.14512 / 0.72 ( 48) hydrogen bonds : bond 0.03064 / 2.10 ( 1320) hydrogen bonds : angle 2.60397 / 1.91 ( 3924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3930.63 seconds wall clock time: 68 minutes 12.76 seconds (4092.76 seconds total)