Starting phenix.real_space_refine on Sat Jul 4 15:16:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqb_23941/07_2026/7mqb_23941.map" } resolution = 3.25 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= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11544 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 48 5.16 5 C 8064 2.51 5 N 2328 2.21 5 O 2304 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 68 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Restraints were copied for chains: C, E, G, I, K, M, O, D, F, H, J, L, N, P Time building chain proxies: 1.85, per 1000 atoms: 0.14 Number of scatterers: 12760 At special positions: 0 Unit cell: (105.4, 105.4, 88.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 P 16 15.00 O 2304 8.00 N 2328 7.00 C 8064 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.06 Conformation dependent library (CDL) restraints added in 487.0 milliseconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 8 sheets defined 45.4% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 155 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 155 Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.887A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 158 through 173 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 71 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 145 through 155 Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 155 Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.886A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 155 Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU A 3 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL A 52 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU C 3 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL C 52 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU E 3 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL E 52 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU G 3 " --> pdb=" O ALA G 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL G 52 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.484A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU M 27 " --> pdb=" O CYS M 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL M 41 " --> pdb=" O ASP M 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASP M 25 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU M 43 " --> pdb=" O ALA M 23 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA M 23 " --> pdb=" O LEU M 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.483A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 560 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 1.36 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: 4216 1.34 - 1.46: 2302 1.46 - 1.57: 6418 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 13024 Sorted by residual: bond pdb=" CG LYS C 103 " pdb=" CD LYS C 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.28e+00 bond pdb=" CG LYS E 103 " pdb=" CD LYS E 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS O 103 " pdb=" CD LYS O 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS I 103 " pdb=" CD LYS I 103 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.26e+00 bond pdb=" CG LYS A 103 " pdb=" CD LYS A 103 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.24e+00 ... (remaining 13019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 15225 0.95 - 1.90: 2092 1.90 - 2.85: 354 2.85 - 3.80: 71 3.80 - 4.75: 34 Bond angle restraints: 17776 Sorted by residual: angle pdb=" C SER E 61 " pdb=" N ALA E 62 " pdb=" CA ALA E 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.55e+01 angle pdb=" C SER C 61 " pdb=" N ALA C 62 " pdb=" CA ALA C 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.55e+01 angle pdb=" C SER A 61 " pdb=" N ALA A 62 " pdb=" CA ALA A 62 " ideal model delta sigma weight residual 122.28 125.74 -3.46 8.80e-01 1.29e+00 1.54e+01 angle pdb=" C SER G 61 " pdb=" N ALA G 62 " pdb=" CA ALA G 62 " ideal model delta sigma weight residual 122.28 125.73 -3.45 8.80e-01 1.29e+00 1.54e+01 angle pdb=" C SER I 61 " pdb=" N ALA I 62 " pdb=" CA ALA I 62 " ideal model delta sigma weight residual 122.28 125.72 -3.44 8.80e-01 1.29e+00 1.53e+01 ... (remaining 17771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 7137 17.25 - 34.50: 451 34.50 - 51.75: 100 51.75 - 69.00: 8 69.00 - 86.25: 16 Dihedral angle restraints: 7712 sinusoidal: 2928 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE M 78 " pdb=" C PHE M 78 " pdb=" N HIS M 79 " pdb=" CA HIS M 79 " ideal model delta harmonic sigma weight residual 180.00 158.03 21.97 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA PHE A 78 " pdb=" C PHE A 78 " pdb=" N HIS A 79 " pdb=" CA HIS A 79 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 978 0.030 - 0.061: 617 0.061 - 0.091: 339 0.091 - 0.121: 157 0.121 - 0.152: 37 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA VAL E 40 " pdb=" N VAL E 40 " pdb=" C VAL E 40 " pdb=" CB VAL E 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA VAL I 40 " pdb=" N VAL I 40 " pdb=" C VAL I 40 " pdb=" CB VAL I 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 chirality pdb=" CA VAL O 40 " pdb=" N VAL O 40 " pdb=" C VAL O 40 " pdb=" CB VAL O 40 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2125 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE K 83 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C PHE K 83 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE K 83 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP K 84 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 83 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE O 83 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE O 83 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP O 84 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " 0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE C 83 " -0.026 2.00e-02 2.50e+03 pdb=" O PHE C 83 " 0.010 2.00e-02 2.50e+03 pdb=" N ASP C 84 " 0.009 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3579 2.82 - 3.34: 11494 3.34 - 3.86: 21299 3.86 - 4.38: 25619 4.38 - 4.90: 43455 Nonbonded interactions: 105446 Sorted by model distance: nonbonded pdb=" NE2 HIS K 79 " pdb=" OP1 G L 603 " model vdw 2.302 3.120 nonbonded pdb=" NE2 HIS A 79 " pdb=" OP1 G B 603 " model vdw 2.341 3.120 nonbonded pdb=" OH TYR M 17 " pdb=" OD2 ASP M 51 " model vdw 2.341 3.040 nonbonded pdb=" OH TYR O 17 " pdb=" OD2 ASP O 51 " model vdw 2.341 3.040 nonbonded pdb=" OH TYR C 17 " pdb=" OD2 ASP C 51 " model vdw 2.341 3.040 ... (remaining 105441 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.034 13024 Z= 0.288 Angle : 0.721 4.752 17776 Z= 0.456 Chirality : 0.052 0.152 2128 Planarity : 0.004 0.021 2200 Dihedral : 13.003 86.249 4592 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.66 % Allowed : 1.32 % Favored : 98.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.20), residues: 1624 helix: 0.73 (0.19), residues: 704 sheet: 0.72 (0.23), residues: 248 loop : 1.33 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 37 TYR 0.006 0.002 TYR M 17 PHE 0.018 0.002 PHE E 78 TRP 0.021 0.003 TRP G 197 HIS 0.004 0.001 HIS G 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.29 (13024) covalent geometry : angle 0.72147 / 0.46 (17776) hydrogen bonds : bond 0.11665 / 8.01 ( 560) hydrogen bonds : angle 7.70024 / 5.57 ( 1680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 0.381 Fit side-chains REVERT: A 51 ASP cc_start: 0.7823 (m-30) cc_final: 0.7491 (m-30) REVERT: A 119 LYS cc_start: 0.8624 (tttm) cc_final: 0.8314 (tttp) REVERT: C 119 LYS cc_start: 0.8704 (tttm) cc_final: 0.8405 (tttp) REVERT: I 51 ASP cc_start: 0.7900 (m-30) cc_final: 0.7616 (m-30) REVERT: K 51 ASP cc_start: 0.7863 (m-30) cc_final: 0.7541 (m-30) REVERT: K 119 LYS cc_start: 0.8611 (tttm) cc_final: 0.8295 (tttp) REVERT: K 138 ASP cc_start: 0.8546 (t0) cc_final: 0.8340 (t0) REVERT: O 119 LYS cc_start: 0.8787 (tttm) cc_final: 0.8481 (tttt) outliers start: 8 outliers final: 0 residues processed: 241 average time/residue: 0.1030 time to fit residues: 36.2507 Evaluate side-chains 193 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 59 GLN C 16 ASN C 59 GLN E 8 GLN E 16 ASN E 59 GLN G 8 GLN G 16 ASN G 59 GLN I 16 ASN I 59 GLN K 16 ASN K 59 GLN M 16 ASN M 59 GLN O 8 GLN O 16 ASN O 59 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.103273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.084590 restraints weight = 16367.569| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.70 r_work: 0.2814 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 13024 Z= 0.099 Angle : 0.435 4.667 17776 Z= 0.239 Chirality : 0.044 0.124 2128 Planarity : 0.003 0.024 2200 Dihedral : 5.351 32.581 1944 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.40 % Allowed : 6.41 % Favored : 92.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.21), residues: 1624 helix: 2.06 (0.20), residues: 704 sheet: 1.07 (0.24), residues: 248 loop : 0.98 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 169 TYR 0.007 0.001 TYR E 158 PHE 0.011 0.001 PHE G 78 TRP 0.004 0.001 TRP I 197 HIS 0.001 0.000 HIS K 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (13024) covalent geometry : angle 0.43452 / 0.24 (17776) hydrogen bonds : bond 0.03438 / 2.37 ( 560) hydrogen bonds : angle 5.94772 / 4.31 ( 1680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 209 time to evaluate : 0.482 Fit side-chains REVERT: A 17 TYR cc_start: 0.9008 (m-80) cc_final: 0.8764 (m-80) REVERT: A 51 ASP cc_start: 0.8600 (m-30) cc_final: 0.8227 (m-30) REVERT: A 119 LYS cc_start: 0.8803 (tttm) cc_final: 0.8494 (tttp) REVERT: C 16 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8420 (t0) REVERT: C 17 TYR cc_start: 0.9013 (m-80) cc_final: 0.8720 (m-80) REVERT: C 115 ARG cc_start: 0.8829 (mtm180) cc_final: 0.8570 (mtm180) REVERT: C 119 LYS cc_start: 0.8885 (tttm) cc_final: 0.8592 (tttp) REVERT: E 51 ASP cc_start: 0.8735 (m-30) cc_final: 0.8352 (m-30) REVERT: E 115 ARG cc_start: 0.8916 (mtm180) cc_final: 0.8610 (mtm180) REVERT: G 51 ASP cc_start: 0.8746 (m-30) cc_final: 0.8280 (m-30) REVERT: I 16 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8432 (t0) REVERT: I 17 TYR cc_start: 0.8989 (m-80) cc_final: 0.8724 (m-80) REVERT: I 51 ASP cc_start: 0.8655 (m-30) cc_final: 0.8270 (m-30) REVERT: I 119 LYS cc_start: 0.8821 (tttm) cc_final: 0.8576 (tttt) REVERT: K 17 TYR cc_start: 0.8990 (m-80) cc_final: 0.8750 (m-80) REVERT: K 51 ASP cc_start: 0.8545 (m-30) cc_final: 0.8189 (m-30) REVERT: K 119 LYS cc_start: 0.8819 (tttm) cc_final: 0.8499 (tttp) REVERT: M 17 TYR cc_start: 0.9015 (m-80) cc_final: 0.8811 (m-80) REVERT: M 119 LYS cc_start: 0.8716 (tttm) cc_final: 0.8462 (tttp) REVERT: O 51 ASP cc_start: 0.8656 (m-30) cc_final: 0.8328 (m-30) REVERT: O 115 ARG cc_start: 0.8831 (mtm180) cc_final: 0.8578 (mtm180) REVERT: O 119 LYS cc_start: 0.8928 (tttm) cc_final: 0.8639 (tttp) outliers start: 17 outliers final: 9 residues processed: 217 average time/residue: 0.1070 time to fit residues: 34.0285 Evaluate side-chains 208 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 147 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.102854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.084127 restraints weight = 16481.119| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.73 r_work: 0.2786 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13024 Z= 0.107 Angle : 0.416 4.548 17776 Z= 0.227 Chirality : 0.044 0.125 2128 Planarity : 0.003 0.024 2200 Dihedral : 4.840 32.544 1944 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.48 % Allowed : 7.89 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.21), residues: 1624 helix: 2.07 (0.20), residues: 704 sheet: 1.30 (0.25), residues: 248 loop : 0.71 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 172 TYR 0.009 0.001 TYR C 17 PHE 0.012 0.001 PHE K 78 TRP 0.004 0.001 TRP M 197 HIS 0.002 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (13024) covalent geometry : angle 0.41562 / 0.23 (17776) hydrogen bonds : bond 0.03270 / 2.26 ( 560) hydrogen bonds : angle 5.55539 / 4.03 ( 1680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8581 (m-30) cc_final: 0.8226 (m-30) REVERT: A 119 LYS cc_start: 0.8914 (tttm) cc_final: 0.8649 (tttp) REVERT: C 16 ASN cc_start: 0.8416 (OUTLIER) cc_final: 0.8098 (t0) REVERT: C 17 TYR cc_start: 0.8976 (m-80) cc_final: 0.8669 (m-80) REVERT: C 25 ASP cc_start: 0.8156 (t70) cc_final: 0.7929 (t0) REVERT: C 115 ARG cc_start: 0.8915 (mtm180) cc_final: 0.8667 (mtm180) REVERT: C 119 LYS cc_start: 0.8921 (tttm) cc_final: 0.8643 (tttt) REVERT: E 51 ASP cc_start: 0.8651 (m-30) cc_final: 0.8371 (m-30) REVERT: E 115 ARG cc_start: 0.8930 (mtm180) cc_final: 0.8720 (mtm180) REVERT: G 25 ASP cc_start: 0.8210 (t70) cc_final: 0.7976 (t0) REVERT: I 16 ASN cc_start: 0.8370 (OUTLIER) cc_final: 0.8066 (t0) REVERT: I 25 ASP cc_start: 0.8152 (t70) cc_final: 0.7941 (t0) REVERT: I 119 LYS cc_start: 0.8856 (tttm) cc_final: 0.8637 (tttt) REVERT: K 51 ASP cc_start: 0.8530 (m-30) cc_final: 0.8188 (m-30) REVERT: K 119 LYS cc_start: 0.8918 (tttm) cc_final: 0.8635 (tttp) REVERT: M 17 TYR cc_start: 0.8982 (m-80) cc_final: 0.8748 (m-80) REVERT: O 25 ASP cc_start: 0.8137 (t70) cc_final: 0.7910 (t0) REVERT: O 51 ASP cc_start: 0.8684 (m-30) cc_final: 0.8391 (m-30) REVERT: O 115 ARG cc_start: 0.8931 (mtm180) cc_final: 0.8726 (mtm180) REVERT: O 119 LYS cc_start: 0.8942 (tttm) cc_final: 0.8681 (tttt) outliers start: 18 outliers final: 9 residues processed: 215 average time/residue: 0.1050 time to fit residues: 32.9679 Evaluate side-chains 211 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 200 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.098811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.080178 restraints weight = 16821.516| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 1.70 r_work: 0.2682 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 13024 Z= 0.229 Angle : 0.491 4.574 17776 Z= 0.265 Chirality : 0.047 0.132 2128 Planarity : 0.004 0.029 2200 Dihedral : 5.072 33.368 1944 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.89 % Allowed : 8.31 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.21), residues: 1624 helix: 1.66 (0.20), residues: 704 sheet: 1.20 (0.28), residues: 240 loop : 0.36 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 169 TYR 0.011 0.001 TYR C 17 PHE 0.014 0.002 PHE M 78 TRP 0.005 0.001 TRP O 197 HIS 0.004 0.001 HIS E 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.23 (13024) covalent geometry : angle 0.49123 / 0.27 (17776) hydrogen bonds : bond 0.04182 / 2.90 ( 560) hydrogen bonds : angle 5.92662 / 4.33 ( 1680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.490 Fit side-chains REVERT: A 25 ASP cc_start: 0.8317 (t70) cc_final: 0.8088 (t0) REVERT: A 119 LYS cc_start: 0.8982 (tttm) cc_final: 0.8726 (tttt) REVERT: C 16 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8233 (t0) REVERT: C 25 ASP cc_start: 0.8355 (t70) cc_final: 0.8141 (t0) REVERT: C 119 LYS cc_start: 0.8984 (tttm) cc_final: 0.8728 (tttt) REVERT: E 51 ASP cc_start: 0.8667 (m-30) cc_final: 0.8363 (m-30) REVERT: G 25 ASP cc_start: 0.8386 (t70) cc_final: 0.8181 (t0) REVERT: G 51 ASP cc_start: 0.8621 (m-30) cc_final: 0.8340 (m-30) REVERT: I 16 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8133 (t0) REVERT: I 25 ASP cc_start: 0.8375 (t70) cc_final: 0.8165 (t0) REVERT: K 25 ASP cc_start: 0.8343 (t70) cc_final: 0.8112 (t0) REVERT: K 119 LYS cc_start: 0.9012 (tttm) cc_final: 0.8767 (tttt) REVERT: M 25 ASP cc_start: 0.8340 (t70) cc_final: 0.8099 (t0) REVERT: O 25 ASP cc_start: 0.8354 (t70) cc_final: 0.8147 (t0) REVERT: O 51 ASP cc_start: 0.8681 (m-30) cc_final: 0.8412 (m-30) REVERT: O 119 LYS cc_start: 0.8991 (tttm) cc_final: 0.8744 (tttt) outliers start: 23 outliers final: 15 residues processed: 204 average time/residue: 0.1030 time to fit residues: 31.4355 Evaluate side-chains 200 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 130 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 157 optimal weight: 7.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.100849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.081514 restraints weight = 16678.367| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.83 r_work: 0.2741 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 13024 Z= 0.157 Angle : 0.430 4.513 17776 Z= 0.234 Chirality : 0.045 0.126 2128 Planarity : 0.003 0.028 2200 Dihedral : 4.873 32.849 1944 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 1.89 % Allowed : 8.80 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.21), residues: 1624 helix: 1.65 (0.20), residues: 704 sheet: 1.29 (0.29), residues: 240 loop : 0.18 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.010 0.001 TYR C 17 PHE 0.010 0.001 PHE O 78 TRP 0.002 0.001 TRP K 197 HIS 0.003 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (13024) covalent geometry : angle 0.43049 / 0.23 (17776) hydrogen bonds : bond 0.03558 / 2.46 ( 560) hydrogen bonds : angle 5.56337 / 4.06 ( 1680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 0.475 Fit side-chains REVERT: C 16 ASN cc_start: 0.8611 (OUTLIER) cc_final: 0.8258 (t0) REVERT: C 17 TYR cc_start: 0.9076 (m-80) cc_final: 0.8792 (m-80) REVERT: C 25 ASP cc_start: 0.8268 (t70) cc_final: 0.8027 (t0) REVERT: E 51 ASP cc_start: 0.8635 (m-30) cc_final: 0.8320 (m-30) REVERT: G 25 ASP cc_start: 0.8352 (t70) cc_final: 0.8147 (t0) REVERT: G 51 ASP cc_start: 0.8624 (m-30) cc_final: 0.8337 (m-30) REVERT: I 16 ASN cc_start: 0.8497 (OUTLIER) cc_final: 0.8213 (t0) REVERT: I 25 ASP cc_start: 0.8281 (t70) cc_final: 0.8045 (t0) REVERT: K 25 ASP cc_start: 0.8300 (t70) cc_final: 0.8066 (t0) REVERT: M 25 ASP cc_start: 0.8297 (t70) cc_final: 0.8050 (t0) REVERT: O 25 ASP cc_start: 0.8283 (t70) cc_final: 0.8047 (t0) REVERT: O 51 ASP cc_start: 0.8671 (m-30) cc_final: 0.8384 (m-30) outliers start: 23 outliers final: 15 residues processed: 206 average time/residue: 0.0987 time to fit residues: 30.5787 Evaluate side-chains 206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 189 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 58 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 78 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.082004 restraints weight = 16682.710| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.72 r_work: 0.2698 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 13024 Z= 0.141 Angle : 0.416 4.521 17776 Z= 0.226 Chirality : 0.044 0.124 2128 Planarity : 0.003 0.027 2200 Dihedral : 4.785 32.825 1944 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.97 % Allowed : 9.54 % Favored : 88.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.21), residues: 1624 helix: 1.68 (0.20), residues: 704 sheet: 1.31 (0.30), residues: 240 loop : 0.05 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 5 TYR 0.008 0.001 TYR C 17 PHE 0.010 0.001 PHE C 78 TRP 0.001 0.001 TRP O 197 HIS 0.003 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (13024) covalent geometry : angle 0.41565 / 0.23 (17776) hydrogen bonds : bond 0.03435 / 2.38 ( 560) hydrogen bonds : angle 5.44077 / 3.97 ( 1680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.455 Fit side-chains REVERT: C 16 ASN cc_start: 0.8628 (OUTLIER) cc_final: 0.8266 (t0) REVERT: E 51 ASP cc_start: 0.8629 (m-30) cc_final: 0.8298 (m-30) REVERT: G 25 ASP cc_start: 0.8308 (t70) cc_final: 0.8056 (t0) REVERT: G 51 ASP cc_start: 0.8632 (m-30) cc_final: 0.8327 (m-30) REVERT: I 16 ASN cc_start: 0.8512 (OUTLIER) cc_final: 0.8217 (t0) REVERT: M 25 ASP cc_start: 0.8280 (t70) cc_final: 0.8048 (t0) REVERT: O 51 ASP cc_start: 0.8649 (m-30) cc_final: 0.8334 (m-30) outliers start: 24 outliers final: 16 residues processed: 200 average time/residue: 0.0950 time to fit residues: 28.4226 Evaluate side-chains 205 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 82 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.079518 restraints weight = 16849.547| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.64 r_work: 0.2726 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 13024 Z= 0.280 Angle : 0.504 4.580 17776 Z= 0.270 Chirality : 0.048 0.136 2128 Planarity : 0.004 0.032 2200 Dihedral : 5.134 32.987 1944 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.97 % Allowed : 9.87 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.20), residues: 1624 helix: 1.40 (0.20), residues: 704 sheet: 0.90 (0.28), residues: 240 loop : -0.23 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 169 TYR 0.007 0.001 TYR I 17 PHE 0.013 0.002 PHE G 78 TRP 0.003 0.001 TRP C 197 HIS 0.004 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.28 (13024) covalent geometry : angle 0.50448 / 0.27 (17776) hydrogen bonds : bond 0.04396 / 3.05 ( 560) hydrogen bonds : angle 5.80936 / 4.25 ( 1680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.433 Fit side-chains REVERT: A 25 ASP cc_start: 0.8401 (t70) cc_final: 0.8159 (t0) REVERT: A 119 LYS cc_start: 0.8960 (tttm) cc_final: 0.8713 (tttt) REVERT: C 16 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8257 (t0) REVERT: C 25 ASP cc_start: 0.8387 (t70) cc_final: 0.8154 (t0) REVERT: C 119 LYS cc_start: 0.8962 (tttm) cc_final: 0.8708 (tttt) REVERT: E 17 TYR cc_start: 0.9231 (m-80) cc_final: 0.8997 (m-80) REVERT: E 51 ASP cc_start: 0.8687 (m-30) cc_final: 0.8482 (m-30) REVERT: E 115 ARG cc_start: 0.9015 (mtm180) cc_final: 0.8805 (mtm180) REVERT: G 25 ASP cc_start: 0.8436 (t70) cc_final: 0.8227 (t0) REVERT: I 16 ASN cc_start: 0.8594 (OUTLIER) cc_final: 0.8238 (t0) REVERT: I 25 ASP cc_start: 0.8392 (t70) cc_final: 0.8180 (t0) REVERT: K 25 ASP cc_start: 0.8405 (t70) cc_final: 0.8162 (t0) REVERT: M 25 ASP cc_start: 0.8441 (t70) cc_final: 0.8225 (t0) REVERT: O 25 ASP cc_start: 0.8376 (t70) cc_final: 0.8155 (t0) REVERT: O 51 ASP cc_start: 0.8720 (m-30) cc_final: 0.8303 (m-30) REVERT: O 115 ARG cc_start: 0.9053 (mtm180) cc_final: 0.8851 (mtm180) REVERT: O 119 LYS cc_start: 0.8974 (tttm) cc_final: 0.8727 (tttt) outliers start: 24 outliers final: 16 residues processed: 200 average time/residue: 0.0971 time to fit residues: 29.3070 Evaluate side-chains 200 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 131 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 131 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 116 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.102739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.084143 restraints weight = 16438.363| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.70 r_work: 0.2764 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2613 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 13024 Z= 0.091 Angle : 0.390 4.514 17776 Z= 0.213 Chirality : 0.043 0.119 2128 Planarity : 0.003 0.026 2200 Dihedral : 4.624 32.623 1944 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % Rotamer: Outliers : 1.07 % Allowed : 10.94 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.21), residues: 1624 helix: 1.72 (0.20), residues: 704 sheet: 1.34 (0.30), residues: 240 loop : -0.22 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 5 TYR 0.012 0.001 TYR I 17 PHE 0.008 0.001 PHE M 78 TRP 0.002 0.000 TRP M 139 HIS 0.002 0.000 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.09 (13024) covalent geometry : angle 0.38965 / 0.21 (17776) hydrogen bonds : bond 0.02924 / 2.02 ( 560) hydrogen bonds : angle 5.21518 / 3.79 ( 1680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.489 Fit side-chains REVERT: A 17 TYR cc_start: 0.9043 (m-80) cc_final: 0.8803 (m-80) REVERT: C 16 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.7992 (t0) REVERT: E 17 TYR cc_start: 0.9112 (m-80) cc_final: 0.8813 (m-80) REVERT: E 51 ASP cc_start: 0.8628 (m-30) cc_final: 0.8352 (m-30) REVERT: E 115 ARG cc_start: 0.9041 (mtm180) cc_final: 0.8785 (mtm180) REVERT: E 119 LYS cc_start: 0.8877 (tttm) cc_final: 0.8653 (tttt) REVERT: G 17 TYR cc_start: 0.9126 (m-80) cc_final: 0.8798 (m-80) REVERT: I 16 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7995 (t0) REVERT: K 17 TYR cc_start: 0.9042 (m-80) cc_final: 0.8793 (m-80) REVERT: K 119 LYS cc_start: 0.8921 (tttm) cc_final: 0.8690 (tttt) REVERT: M 17 TYR cc_start: 0.9015 (m-80) cc_final: 0.8812 (m-80) REVERT: O 17 TYR cc_start: 0.9116 (m-80) cc_final: 0.8598 (m-80) REVERT: O 51 ASP cc_start: 0.8631 (m-30) cc_final: 0.8294 (m-30) REVERT: O 115 ARG cc_start: 0.9040 (mtm180) cc_final: 0.8787 (mtm180) outliers start: 13 outliers final: 5 residues processed: 206 average time/residue: 0.0986 time to fit residues: 30.2685 Evaluate side-chains 196 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 189 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain M residue 131 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 155 optimal weight: 0.0570 chunk 33 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.081678 restraints weight = 16679.215| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.69 r_work: 0.2706 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 13024 Z= 0.156 Angle : 0.427 4.549 17776 Z= 0.229 Chirality : 0.045 0.124 2128 Planarity : 0.003 0.028 2200 Dihedral : 4.756 32.826 1944 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.23 % Allowed : 11.27 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.21), residues: 1624 helix: 1.61 (0.20), residues: 712 sheet: 1.27 (0.30), residues: 240 loop : -0.17 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 67 TYR 0.006 0.001 TYR C 17 PHE 0.011 0.001 PHE A 78 TRP 0.002 0.001 TRP C 197 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (13024) covalent geometry : angle 0.42721 / 0.23 (17776) hydrogen bonds : bond 0.03526 / 2.45 ( 560) hydrogen bonds : angle 5.36442 / 3.91 ( 1680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.445 Fit side-chains REVERT: A 25 ASP cc_start: 0.8348 (t70) cc_final: 0.8093 (t0) REVERT: C 16 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8315 (t0) REVERT: C 25 ASP cc_start: 0.8318 (t70) cc_final: 0.8051 (t0) REVERT: C 115 ARG cc_start: 0.9042 (mtm180) cc_final: 0.8840 (mtm180) REVERT: E 17 TYR cc_start: 0.9087 (m-80) cc_final: 0.8739 (m-80) REVERT: E 25 ASP cc_start: 0.8315 (t70) cc_final: 0.8054 (t0) REVERT: E 51 ASP cc_start: 0.8648 (m-30) cc_final: 0.8377 (m-30) REVERT: G 25 ASP cc_start: 0.8371 (t70) cc_final: 0.8148 (t0) REVERT: I 16 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8289 (t0) REVERT: I 25 ASP cc_start: 0.8333 (t70) cc_final: 0.8068 (t0) REVERT: K 25 ASP cc_start: 0.8306 (t70) cc_final: 0.8065 (t0) REVERT: K 119 LYS cc_start: 0.8934 (tttm) cc_final: 0.8708 (tttt) REVERT: M 25 ASP cc_start: 0.8340 (t70) cc_final: 0.8079 (t0) REVERT: O 25 ASP cc_start: 0.8294 (t70) cc_final: 0.8030 (t0) REVERT: O 51 ASP cc_start: 0.8657 (m-30) cc_final: 0.8283 (m-30) outliers start: 15 outliers final: 7 residues processed: 190 average time/residue: 0.1000 time to fit residues: 28.2324 Evaluate side-chains 193 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 184 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 108 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 127 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN O 16 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.080852 restraints weight = 16863.560| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 1.70 r_work: 0.2680 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 13024 Z= 0.199 Angle : 0.454 4.541 17776 Z= 0.243 Chirality : 0.046 0.127 2128 Planarity : 0.003 0.029 2200 Dihedral : 4.904 32.875 1944 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.73 % Allowed : 10.94 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1624 helix: 1.56 (0.20), residues: 704 sheet: 1.12 (0.30), residues: 240 loop : -0.36 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 67 TYR 0.006 0.001 TYR C 17 PHE 0.012 0.002 PHE M 78 TRP 0.002 0.001 TRP G 139 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.20 (13024) covalent geometry : angle 0.45419 / 0.24 (17776) hydrogen bonds : bond 0.03790 / 2.63 ( 560) hydrogen bonds : angle 5.49934 / 4.02 ( 1680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.495 Fit side-chains REVERT: A 25 ASP cc_start: 0.8435 (t70) cc_final: 0.8186 (t0) REVERT: C 16 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8283 (t0) REVERT: C 25 ASP cc_start: 0.8402 (t70) cc_final: 0.8156 (t0) REVERT: C 115 ARG cc_start: 0.9024 (mtm180) cc_final: 0.8818 (mtm180) REVERT: E 17 TYR cc_start: 0.9106 (m-80) cc_final: 0.8738 (m-80) REVERT: E 25 ASP cc_start: 0.8385 (t70) cc_final: 0.8149 (t0) REVERT: E 51 ASP cc_start: 0.8645 (m-30) cc_final: 0.8394 (m-30) REVERT: G 25 ASP cc_start: 0.8464 (t70) cc_final: 0.8224 (t0) REVERT: I 16 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8212 (t0) REVERT: I 25 ASP cc_start: 0.8408 (t70) cc_final: 0.8172 (t0) REVERT: K 25 ASP cc_start: 0.8401 (t70) cc_final: 0.8170 (t0) REVERT: K 119 LYS cc_start: 0.8943 (tttm) cc_final: 0.8705 (tttt) REVERT: M 25 ASP cc_start: 0.8424 (t70) cc_final: 0.8176 (t0) REVERT: O 25 ASP cc_start: 0.8392 (t70) cc_final: 0.8154 (t0) REVERT: O 51 ASP cc_start: 0.8682 (m-30) cc_final: 0.8311 (m-30) outliers start: 21 outliers final: 13 residues processed: 206 average time/residue: 0.0959 time to fit residues: 29.6880 Evaluate side-chains 206 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 191 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 131 SER Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 16 ASN Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 154 SER Chi-restraints excluded: chain K residue 154 SER Chi-restraints excluded: chain M residue 131 SER Chi-restraints excluded: chain M residue 154 SER Chi-restraints excluded: chain O residue 154 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 49 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 15 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 16 ASN A 32 GLN C 16 ASN C 32 GLN E 16 ASN E 32 GLN G 16 ASN G 32 GLN I 16 ASN I 32 GLN K 16 ASN K 32 GLN M 16 ASN M 32 GLN O 16 ASN O 32 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.099126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.080352 restraints weight = 16813.927| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.69 r_work: 0.2679 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 13024 Z= 0.219 Angle : 0.465 4.546 17776 Z= 0.248 Chirality : 0.046 0.128 2128 Planarity : 0.003 0.030 2200 Dihedral : 4.975 32.925 1944 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 1.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.81 % Allowed : 11.10 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1624 helix: 1.50 (0.20), residues: 704 sheet: 0.98 (0.30), residues: 240 loop : -0.41 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 169 TYR 0.010 0.001 TYR C 17 PHE 0.012 0.002 PHE K 78 TRP 0.003 0.001 TRP G 139 HIS 0.003 0.001 HIS A 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (13024) covalent geometry : angle 0.46465 / 0.25 (17776) hydrogen bonds : bond 0.03922 / 2.72 ( 560) hydrogen bonds : angle 5.57602 / 4.07 ( 1680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2410.44 seconds wall clock time: 42 minutes 9.10 seconds (2529.10 seconds total)