Starting phenix.real_space_refine on Thu Jul 2 03:10:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wl8_66049/07_2026/9wl8_66049.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wl8_66049/07_2026/9wl8_66049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wl8_66049/07_2026/9wl8_66049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wl8_66049/07_2026/9wl8_66049.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wl8_66049/07_2026/9wl8_66049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wl8_66049/07_2026/9wl8_66049.map" } resolution = 3.09 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= 0.001 sd= 0.004 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 48 5.16 5 C 3846 2.51 5 N 1116 2.21 5 O 1122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6132 Number of models: 1 Model: "" Number of chains: 1 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1022 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 123} Restraints were copied for chains: A, B, C, D, E Time building chain proxies: 1.18, per 1000 atoms: 0.19 Number of scatterers: 6132 At special positions: 0 Unit cell: (155.31, 128.34, 41.85, 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 48 16.00 O 1122 8.00 N 1116 7.00 C 3846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 42 " distance=2.03 Simple disulfide: pdb=" SG CYS F 18 " - pdb=" SG CYS F 23 " distance=2.03 Simple disulfide: pdb=" SG CYS F 81 " - pdb=" SG CYS F 124 " distance=2.03 Simple disulfide: pdb=" SG CYS A 7 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS B 7 " - pdb=" SG CYS B 42 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 42 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 42 " distance=2.03 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 23 " distance=2.03 Simple disulfide: pdb=" SG CYS B 18 " - pdb=" SG CYS B 23 " distance=2.03 Simple disulfide: pdb=" SG CYS C 18 " - pdb=" SG CYS C 23 " distance=2.03 Simple disulfide: pdb=" SG CYS D 18 " - pdb=" SG CYS D 23 " distance=2.03 Simple disulfide: pdb=" SG CYS E 18 " - pdb=" SG CYS E 23 " distance=2.03 Simple disulfide: pdb=" SG CYS A 81 " - pdb=" SG CYS A 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 81 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 81 " - pdb=" SG CYS C 124 " distance=2.03 Simple disulfide: pdb=" SG CYS D 81 " - pdb=" SG CYS D 124 " distance=2.03 Simple disulfide: pdb=" SG CYS E 81 " - pdb=" SG CYS E 124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 182.6 milliseconds 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 26 sheets defined 0.0% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 removed outlier: 6.962A pdb=" N ILE B 6 " --> pdb=" O ASN F 5 " (cutoff:3.500A) removed outlier: 8.564A pdb=" N ALA F 4 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 12 through 19 removed outlier: 6.872A pdb=" N ASP F 19 " --> pdb=" O CYS B 18 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER F 12 " --> pdb=" O ASN D 13 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ILE D 15 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU F 14 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR D 17 " --> pdb=" O GLU F 14 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ARG F 16 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP D 19 " --> pdb=" O ARG F 16 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N CYS F 18 " --> pdb=" O ASP D 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.327A pdb=" N TYR F 26 " --> pdb=" O SER B 27 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N GLN B 29 " --> pdb=" O TYR F 26 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA F 28 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 41 removed outlier: 5.737A pdb=" N ASP F 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP D 39 " --> pdb=" O VAL F 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 49 removed outlier: 6.559A pdb=" N VAL F 48 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 60 removed outlier: 9.212A pdb=" N PHE F 52 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 10.767A pdb=" N MET B 55 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N GLY F 54 " --> pdb=" O MET B 55 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N VAL B 57 " --> pdb=" O GLY F 54 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE F 56 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN B 59 " --> pdb=" O ILE F 56 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLY F 58 " --> pdb=" O GLN B 59 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR F 53 " --> pdb=" O PHE D 52 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLY D 54 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET F 55 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 56 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN F 59 " --> pdb=" O GLY D 58 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLU D 60 " --> pdb=" O GLN F 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 66 through 75 removed outlier: 6.307A pdb=" N ASN F 67 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN B 70 " --> pdb=" O ASN F 67 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE F 69 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLY B 72 " --> pdb=" O ILE F 69 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ASN F 71 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ARG B 74 " --> pdb=" O ASN F 71 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL F 73 " --> pdb=" O ARG B 74 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL D 73 " --> pdb=" O GLY F 72 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ARG F 74 " --> pdb=" O VAL D 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 87 removed outlier: 6.230A pdb=" N MET F 84 " --> pdb=" O PHE B 85 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE B 87 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TYR F 86 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.185A pdb=" N ILE F 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.580A pdb=" N THR F 104 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.771A pdb=" N VAL F 111 " --> pdb=" O LYS B 110 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU F 108 " --> pdb=" O GLN D 109 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N VAL D 111 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS F 110 " --> pdb=" O VAL D 111 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 114 through 115 removed outlier: 6.843A pdb=" N GLY F 114 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 119 through 125 removed outlier: 6.783A pdb=" N ASP B 125 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL F 119 " --> pdb=" O HIS D 120 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLU D 122 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE F 121 " --> pdb=" O GLU D 122 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N CYS D 124 " --> pdb=" O ILE F 121 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N ASN F 123 " --> pdb=" O CYS D 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 3 through 6 removed outlier: 6.988A pdb=" N ILE C 6 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ALA A 4 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 12 through 19 removed outlier: 6.886A pdb=" N ASP A 19 " --> pdb=" O CYS C 18 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N SER A 12 " --> pdb=" O ASN E 13 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE E 15 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU A 14 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N THR E 17 " --> pdb=" O GLU A 14 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 16 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP E 19 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS A 18 " --> pdb=" O ASP E 19 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 26 through 29 removed outlier: 6.329A pdb=" N TYR A 26 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN C 29 " --> pdb=" O TYR A 26 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA A 28 " --> pdb=" O GLN C 29 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 38 through 41 removed outlier: 5.741A pdb=" N ASP A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP E 39 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 47 through 49 removed outlier: 6.565A pdb=" N VAL A 48 " --> pdb=" O TYR E 49 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 52 through 60 removed outlier: 9.218A pdb=" N PHE A 52 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 10.771A pdb=" N MET C 55 " --> pdb=" O PHE A 52 " (cutoff:3.500A) removed outlier: 9.088A pdb=" N GLY A 54 " --> pdb=" O MET C 55 " (cutoff:3.500A) removed outlier: 9.702A pdb=" N VAL C 57 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N ILE A 56 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N GLN C 59 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLY A 58 " --> pdb=" O GLN C 59 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR A 53 " --> pdb=" O PHE E 52 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLY E 54 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET A 55 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE E 56 " --> pdb=" O MET A 55 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLN A 59 " --> pdb=" O GLY E 58 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU E 60 " --> pdb=" O GLN A 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.279A pdb=" N ASN A 67 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASN C 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 69 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N GLY C 72 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N ASN A 71 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N ARG C 74 " --> pdb=" O ASN A 71 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N VAL A 73 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL E 73 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ARG A 74 " --> pdb=" O VAL E 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 83 through 87 removed outlier: 6.205A pdb=" N MET A 84 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N ILE C 87 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TYR A 86 " --> pdb=" O ILE C 87 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 96 through 98 removed outlier: 6.184A pdb=" N ILE A 96 " --> pdb=" O LYS E 97 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 104 through 105 removed outlier: 6.589A pdb=" N THR A 104 " --> pdb=" O LEU E 105 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 108 through 111 removed outlier: 6.776A pdb=" N VAL A 111 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU A 108 " --> pdb=" O GLN E 109 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL E 111 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LYS A 110 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.855A pdb=" N GLY A 114 " --> pdb=" O ILE C 115 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 119 through 125 removed outlier: 6.784A pdb=" N ASP C 125 " --> pdb=" O CYS A 124 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL A 119 " --> pdb=" O HIS E 120 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLU E 122 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE A 121 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N CYS E 124 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N ASN A 123 " --> pdb=" O CYS E 124 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 234 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: 0.83 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2028 1.35 - 1.46: 1305 1.46 - 1.58: 2883 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 6276 Sorted by residual: bond pdb=" CA LYS F 91 " pdb=" CB LYS F 91 " ideal model delta sigma weight residual 1.528 1.540 -0.013 1.33e-02 5.65e+03 9.00e-01 bond pdb=" CA LYS E 91 " pdb=" CB LYS E 91 " ideal model delta sigma weight residual 1.528 1.540 -0.013 1.33e-02 5.65e+03 8.96e-01 bond pdb=" CA ALA B 44 " pdb=" C ALA B 44 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 8.80e-01 bond pdb=" CA LYS B 91 " pdb=" CB LYS B 91 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.33e-02 5.65e+03 8.72e-01 bond pdb=" CA LYS A 91 " pdb=" CB LYS A 91 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.33e-02 5.65e+03 8.68e-01 ... (remaining 6271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 7920 1.41 - 2.81: 414 2.81 - 4.22: 93 4.22 - 5.63: 27 5.63 - 7.04: 18 Bond angle restraints: 8472 Sorted by residual: angle pdb=" N HIS F 118 " pdb=" CA HIS F 118 " pdb=" C HIS F 118 " ideal model delta sigma weight residual 110.91 114.73 -3.82 1.17e+00 7.31e-01 1.07e+01 angle pdb=" N HIS A 118 " pdb=" CA HIS A 118 " pdb=" C HIS A 118 " ideal model delta sigma weight residual 110.91 114.71 -3.80 1.17e+00 7.31e-01 1.06e+01 angle pdb=" N HIS D 118 " pdb=" CA HIS D 118 " pdb=" C HIS D 118 " ideal model delta sigma weight residual 110.91 114.71 -3.80 1.17e+00 7.31e-01 1.05e+01 angle pdb=" N HIS B 118 " pdb=" CA HIS B 118 " pdb=" C HIS B 118 " ideal model delta sigma weight residual 110.91 114.71 -3.80 1.17e+00 7.31e-01 1.05e+01 angle pdb=" N HIS E 118 " pdb=" CA HIS E 118 " pdb=" C HIS E 118 " ideal model delta sigma weight residual 110.91 114.70 -3.79 1.17e+00 7.31e-01 1.05e+01 ... (remaining 8467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.11: 3349 16.11 - 32.23: 323 32.23 - 48.34: 120 48.34 - 64.45: 42 64.45 - 80.56: 12 Dihedral angle restraints: 3846 sinusoidal: 1596 harmonic: 2250 Sorted by residual: dihedral pdb=" CA VAL A 119 " pdb=" C VAL A 119 " pdb=" N HIS A 120 " pdb=" CA HIS A 120 " ideal model delta harmonic sigma weight residual -180.00 -159.38 -20.62 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA VAL E 119 " pdb=" C VAL E 119 " pdb=" N HIS E 120 " pdb=" CA HIS E 120 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA VAL C 119 " pdb=" C VAL C 119 " pdb=" N HIS C 120 " pdb=" CA HIS C 120 " ideal model delta harmonic sigma weight residual -180.00 -159.45 -20.55 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 3843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 496 0.033 - 0.066: 242 0.066 - 0.099: 33 0.099 - 0.132: 103 0.132 - 0.165: 8 Chirality restraints: 882 Sorted by residual: chirality pdb=" CA ARG E 33 " pdb=" N ARG E 33 " pdb=" C ARG E 33 " pdb=" CB ARG E 33 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ARG D 33 " pdb=" N ARG D 33 " pdb=" C ARG D 33 " pdb=" CB ARG D 33 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.84e-01 chirality pdb=" CA ARG A 33 " pdb=" N ARG A 33 " pdb=" C ARG A 33 " pdb=" CB ARG A 33 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.78e-01 ... (remaining 879 not shown) Planarity restraints: 1116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 91 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C LYS A 91 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS A 91 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 91 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" C LYS C 91 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS C 91 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR C 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 91 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LYS D 91 " 0.028 2.00e-02 2.50e+03 pdb=" O LYS D 91 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR D 92 " -0.009 2.00e-02 2.50e+03 ... (remaining 1113 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 2046 2.87 - 3.38: 5291 3.38 - 3.89: 10862 3.89 - 4.39: 11423 4.39 - 4.90: 21553 Nonbonded interactions: 51175 Sorted by model distance: nonbonded pdb=" NZ LYS B 110 " pdb=" OD2 ASP B 125 " model vdw 2.365 3.120 nonbonded pdb=" NZ LYS C 110 " pdb=" OD2 ASP C 125 " model vdw 2.366 3.120 nonbonded pdb=" NZ LYS D 110 " pdb=" OD2 ASP D 125 " model vdw 2.366 3.120 nonbonded pdb=" NZ LYS E 110 " pdb=" OD2 ASP E 125 " model vdw 2.366 3.120 nonbonded pdb=" NZ LYS A 110 " pdb=" OD2 ASP A 125 " model vdw 2.367 3.120 ... (remaining 51170 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: 0.02 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.780 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 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 0.026 6294 Z= 0.165 Angle : 0.827 7.037 8508 Z= 0.450 Chirality : 0.054 0.165 882 Planarity : 0.004 0.024 1116 Dihedral : 16.255 80.565 2376 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 0.00 % Allowed : 17.12 % Favored : 82.88 % 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: -3.94 (0.21), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.16), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 74 TYR 0.016 0.002 TYR A 92 PHE 0.016 0.002 PHE E 85 TRP 0.003 0.001 TRP B 3 HIS 0.011 0.005 HIS C 120 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 ( 6276) covalent geometry : angle 0.82598 / 0.45 ( 8472) SS BOND : bond 0.00245 / 0.17 ( 18) SS BOND : angle 1.09998 / 0.76 ( 36) hydrogen bonds : bond 0.16580 / 11.66 ( 78) hydrogen bonds : angle 8.57123 / 6.06 ( 234) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.238 Fit side-chains REVERT: F 55 MET cc_start: 0.8483 (ttp) cc_final: 0.8257 (ttp) REVERT: F 93 LYS cc_start: 0.6968 (mttt) cc_final: 0.6730 (mtpt) REVERT: F 128 ASP cc_start: 0.8279 (m-30) cc_final: 0.8001 (m-30) REVERT: A 93 LYS cc_start: 0.7042 (mttt) cc_final: 0.6754 (mtpt) REVERT: B 33 ARG cc_start: 0.8557 (mmm160) cc_final: 0.6783 (mmt-90) REVERT: C 33 ARG cc_start: 0.8608 (mmm160) cc_final: 0.7028 (mpt180) REVERT: C 93 LYS cc_start: 0.6978 (mttt) cc_final: 0.6750 (mtpt) REVERT: C 110 LYS cc_start: 0.8821 (tttp) cc_final: 0.8483 (mtpp) REVERT: C 123 ASN cc_start: 0.8338 (m110) cc_final: 0.8040 (m-40) REVERT: D 93 LYS cc_start: 0.7597 (mttt) cc_final: 0.7373 (mtpt) REVERT: D 105 LEU cc_start: 0.8385 (tp) cc_final: 0.8105 (tp) REVERT: E 61 LYS cc_start: 0.8018 (mttt) cc_final: 0.7786 (mttm) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1282 time to fit residues: 19.9812 Evaluate side-chains 88 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 21 HIS F 67 ASN F 123 ASN A 21 HIS A 25 GLN A 67 ASN A 116 GLN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN B 25 GLN B 67 ASN B 116 GLN B 123 ASN C 25 GLN C 67 ASN C 123 ASN D 21 HIS D 25 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN D 123 ASN E 21 HIS E 25 GLN E 29 GLN ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 ASN E 116 GLN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 123 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.139358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.126763 restraints weight = 8073.450| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 1.48 r_work: 0.3709 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 6294 Z= 0.311 Angle : 0.841 7.241 8508 Z= 0.444 Chirality : 0.057 0.153 882 Planarity : 0.005 0.029 1116 Dihedral : 6.430 28.734 876 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 1.35 % Allowed : 19.52 % Favored : 79.13 % 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: -3.79 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 30 TYR 0.028 0.004 TYR D 86 PHE 0.013 0.002 PHE D 85 TRP 0.006 0.002 TRP D 3 HIS 0.011 0.005 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.31 ( 6276) covalent geometry : angle 0.83716 / 0.44 ( 8472) SS BOND : bond 0.00482 / 0.29 ( 18) SS BOND : angle 1.43955 / 1.04 ( 36) hydrogen bonds : bond 0.03455 / 2.39 ( 78) hydrogen bonds : angle 5.48319 / 3.70 ( 234) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.193 Fit side-chains REVERT: F 93 LYS cc_start: 0.7386 (mttt) cc_final: 0.6897 (mtpt) REVERT: F 128 ASP cc_start: 0.8324 (m-30) cc_final: 0.8025 (m-30) REVERT: A 93 LYS cc_start: 0.7451 (mttt) cc_final: 0.6998 (mtpt) REVERT: A 128 ASP cc_start: 0.8320 (m-30) cc_final: 0.7820 (m-30) REVERT: C 33 ARG cc_start: 0.8808 (mmm160) cc_final: 0.7208 (mpt180) REVERT: C 83 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7416 (tptt) REVERT: C 93 LYS cc_start: 0.7344 (mttt) cc_final: 0.6983 (mtpt) REVERT: C 128 ASP cc_start: 0.7949 (m-30) cc_final: 0.7302 (p0) REVERT: D 20 ARG cc_start: 0.7758 (mtt180) cc_final: 0.5622 (ttp-170) REVERT: D 83 LYS cc_start: 0.8061 (ttmt) cc_final: 0.7390 (tptt) REVERT: D 93 LYS cc_start: 0.7963 (mttt) cc_final: 0.7587 (mtpt) outliers start: 9 outliers final: 9 residues processed: 112 average time/residue: 0.1318 time to fit residues: 17.4469 Evaluate side-chains 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 39 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 21 HIS F 25 GLN ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 21 HIS A 29 GLN A 116 GLN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.139838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.127576 restraints weight = 8070.445| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.51 r_work: 0.3686 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3594 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6294 Z= 0.216 Angle : 0.718 6.156 8508 Z= 0.382 Chirality : 0.054 0.153 882 Planarity : 0.004 0.025 1116 Dihedral : 6.247 30.855 876 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 1.95 % Allowed : 18.02 % Favored : 80.03 % 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: -3.78 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 20 TYR 0.021 0.003 TYR D 86 PHE 0.010 0.002 PHE E 85 TRP 0.004 0.001 TRP F 3 HIS 0.009 0.004 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 ( 6276) covalent geometry : angle 0.71609 / 0.38 ( 8472) SS BOND : bond 0.00422 / 0.26 ( 18) SS BOND : angle 1.12146 / 0.82 ( 36) hydrogen bonds : bond 0.02516 / 1.73 ( 78) hydrogen bonds : angle 5.12866 / 3.49 ( 234) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.241 Fit side-chains REVERT: F 128 ASP cc_start: 0.8364 (m-30) cc_final: 0.8038 (m-30) REVERT: A 116 GLN cc_start: 0.8167 (mt0) cc_final: 0.7862 (mt0) REVERT: A 128 ASP cc_start: 0.8284 (m-30) cc_final: 0.7970 (m-30) REVERT: C 20 ARG cc_start: 0.7922 (mtt180) cc_final: 0.6778 (mmt-90) REVERT: C 33 ARG cc_start: 0.8807 (mmm160) cc_final: 0.7182 (mpt180) REVERT: D 20 ARG cc_start: 0.7829 (mtt180) cc_final: 0.5583 (ttp-170) REVERT: D 84 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7554 (tmm) REVERT: D 128 ASP cc_start: 0.8271 (m-30) cc_final: 0.7664 (p0) outliers start: 13 outliers final: 12 residues processed: 93 average time/residue: 0.0904 time to fit residues: 10.8649 Evaluate side-chains 96 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 44 optimal weight: 0.2980 chunk 17 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 21 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 74 optimal weight: 9.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 21 HIS A 21 HIS A 29 GLN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130283 restraints weight = 8005.659| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 1.51 r_work: 0.3733 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3642 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6294 Z= 0.130 Angle : 0.631 5.300 8508 Z= 0.335 Chirality : 0.052 0.145 882 Planarity : 0.003 0.024 1116 Dihedral : 5.964 29.710 876 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.65 % Allowed : 17.72 % Favored : 80.63 % 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: -3.70 (0.23), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 20 TYR 0.019 0.002 TYR D 86 PHE 0.009 0.001 PHE E 85 TRP 0.003 0.001 TRP F 3 HIS 0.007 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 6276) covalent geometry : angle 0.62931 / 0.33 ( 8472) SS BOND : bond 0.00293 / 0.18 ( 18) SS BOND : angle 0.92838 / 0.68 ( 36) hydrogen bonds : bond 0.01787 / 1.18 ( 78) hydrogen bonds : angle 4.85766 / 3.32 ( 234) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.254 Fit side-chains REVERT: F 128 ASP cc_start: 0.8301 (m-30) cc_final: 0.7997 (m-30) REVERT: A 116 GLN cc_start: 0.8124 (mt0) cc_final: 0.7811 (mt0) REVERT: C 20 ARG cc_start: 0.7931 (mtt180) cc_final: 0.6739 (mmt-90) REVERT: C 33 ARG cc_start: 0.8773 (mmm160) cc_final: 0.6731 (mmt-90) REVERT: C 84 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7514 (ttm) REVERT: C 128 ASP cc_start: 0.7883 (m-30) cc_final: 0.7635 (p0) REVERT: D 84 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7516 (tmm) REVERT: D 128 ASP cc_start: 0.8314 (m-30) cc_final: 0.7728 (p0) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.0728 time to fit residues: 9.0064 Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 72 optimal weight: 8.9990 chunk 61 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS A 29 GLN ** A 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 ASN E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** E 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.140076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.127507 restraints weight = 8193.549| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.54 r_work: 0.3700 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6294 Z= 0.193 Angle : 0.684 6.240 8508 Z= 0.362 Chirality : 0.053 0.142 882 Planarity : 0.003 0.027 1116 Dihedral : 6.017 29.247 876 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 3.15 % Allowed : 16.67 % Favored : 80.18 % 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: -3.75 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 20 TYR 0.021 0.003 TYR D 86 PHE 0.014 0.002 PHE D 85 TRP 0.003 0.001 TRP C 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.19 ( 6276) covalent geometry : angle 0.68186 / 0.36 ( 8472) SS BOND : bond 0.00399 / 0.24 ( 18) SS BOND : angle 1.07840 / 0.79 ( 36) hydrogen bonds : bond 0.02071 / 1.40 ( 78) hydrogen bonds : angle 4.73491 / 3.21 ( 234) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.198 Fit side-chains REVERT: F 128 ASP cc_start: 0.8259 (m-30) cc_final: 0.7989 (m-30) REVERT: A 84 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7831 (ttm) REVERT: B 20 ARG cc_start: 0.8138 (mtt180) cc_final: 0.6769 (mmt-90) REVERT: C 20 ARG cc_start: 0.8079 (mtt180) cc_final: 0.6891 (mmt-90) REVERT: C 33 ARG cc_start: 0.8795 (mmm160) cc_final: 0.6728 (mmt-90) REVERT: C 84 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7509 (ttm) REVERT: D 20 ARG cc_start: 0.7823 (mtt180) cc_final: 0.5592 (ttp-170) REVERT: D 84 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7485 (tmm) REVERT: D 128 ASP cc_start: 0.8310 (m-30) cc_final: 0.8086 (m-30) REVERT: E 83 LYS cc_start: 0.8199 (ttmt) cc_final: 0.7476 (tptt) outliers start: 21 outliers final: 15 residues processed: 99 average time/residue: 0.0959 time to fit residues: 12.1796 Evaluate side-chains 102 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 52 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 67 ASN A 21 HIS A 29 GLN A 116 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN ** E 120 HIS ** 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 = 0.3896 r_free = 0.3896 target = 0.137926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.125339 restraints weight = 8157.769| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.52 r_work: 0.3666 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 6294 Z= 0.242 Angle : 0.725 6.214 8508 Z= 0.385 Chirality : 0.054 0.150 882 Planarity : 0.004 0.031 1116 Dihedral : 6.178 29.669 876 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 3.15 % Allowed : 16.22 % Favored : 80.63 % 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: -3.84 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 20 TYR 0.021 0.003 TYR D 86 PHE 0.015 0.002 PHE D 85 TRP 0.004 0.001 TRP B 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 ( 6276) covalent geometry : angle 0.72207 / 0.38 ( 8472) SS BOND : bond 0.00463 / 0.28 ( 18) SS BOND : angle 1.16494 / 0.85 ( 36) hydrogen bonds : bond 0.02240 / 1.51 ( 78) hydrogen bonds : angle 4.70872 / 3.19 ( 234) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.275 Fit side-chains REVERT: A 84 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7901 (ttm) REVERT: A 116 GLN cc_start: 0.8230 (mt0) cc_final: 0.7938 (mt0) REVERT: C 20 ARG cc_start: 0.8119 (mtt180) cc_final: 0.6942 (mmt-90) REVERT: C 33 ARG cc_start: 0.8806 (mmm160) cc_final: 0.7203 (mpt180) REVERT: C 84 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: D 20 ARG cc_start: 0.7845 (mtt180) cc_final: 0.5686 (ttp-170) REVERT: D 84 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7386 (ttm) REVERT: D 128 ASP cc_start: 0.8316 (m-30) cc_final: 0.8101 (m-30) outliers start: 21 outliers final: 14 residues processed: 89 average time/residue: 0.0833 time to fit residues: 9.7898 Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 19 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.141168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.128720 restraints weight = 8068.312| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 1.51 r_work: 0.3718 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6294 Z= 0.141 Angle : 0.640 5.227 8508 Z= 0.341 Chirality : 0.052 0.144 882 Planarity : 0.003 0.028 1116 Dihedral : 5.907 27.534 876 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.55 % Allowed : 16.82 % Favored : 80.63 % 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: -3.77 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 20 TYR 0.018 0.002 TYR D 86 PHE 0.015 0.001 PHE D 85 TRP 0.003 0.001 TRP F 3 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 6276) covalent geometry : angle 0.63788 / 0.34 ( 8472) SS BOND : bond 0.00338 / 0.20 ( 18) SS BOND : angle 0.99428 / 0.72 ( 36) hydrogen bonds : bond 0.01750 / 1.17 ( 78) hydrogen bonds : angle 4.64329 / 3.16 ( 234) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.228 Fit side-chains REVERT: A 84 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.8021 (ttm) REVERT: C 20 ARG cc_start: 0.8109 (mtt180) cc_final: 0.6941 (mmt-90) REVERT: C 33 ARG cc_start: 0.8781 (mmm160) cc_final: 0.6699 (mmt-90) REVERT: C 84 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7292 (ttm) REVERT: D 84 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7490 (tmm) outliers start: 17 outliers final: 11 residues processed: 91 average time/residue: 0.0850 time to fit residues: 10.1467 Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS A 29 GLN A 116 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.141084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.128502 restraints weight = 8088.236| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.52 r_work: 0.3716 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6294 Z= 0.155 Angle : 0.650 5.345 8508 Z= 0.345 Chirality : 0.053 0.142 882 Planarity : 0.003 0.026 1116 Dihedral : 5.848 26.766 876 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 2.70 % Allowed : 17.27 % Favored : 80.03 % 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: -3.75 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 20 TYR 0.018 0.003 TYR D 86 PHE 0.016 0.001 PHE D 85 TRP 0.003 0.001 TRP C 3 HIS 0.008 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 ( 6276) covalent geometry : angle 0.64780 / 0.34 ( 8472) SS BOND : bond 0.00351 / 0.21 ( 18) SS BOND : angle 1.00147 / 0.72 ( 36) hydrogen bonds : bond 0.01806 / 1.21 ( 78) hydrogen bonds : angle 4.58021 / 3.12 ( 234) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.238 Fit side-chains REVERT: F 128 ASP cc_start: 0.8531 (m-30) cc_final: 0.8293 (m-30) REVERT: A 116 GLN cc_start: 0.8131 (mt0) cc_final: 0.7834 (mt0) REVERT: C 20 ARG cc_start: 0.8092 (mtt180) cc_final: 0.6882 (mmt-90) REVERT: C 33 ARG cc_start: 0.8773 (mmm160) cc_final: 0.6619 (mmt-90) REVERT: C 84 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7276 (ttm) REVERT: D 84 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7438 (tmm) REVERT: D 128 ASP cc_start: 0.8409 (m-30) cc_final: 0.7880 (p0) outliers start: 18 outliers final: 16 residues processed: 87 average time/residue: 0.0765 time to fit residues: 9.0099 Evaluate side-chains 97 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 35 HIS Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS A 29 GLN A 64 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.143543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131105 restraints weight = 8003.764| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.51 r_work: 0.3755 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3664 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6294 Z= 0.115 Angle : 0.608 4.973 8508 Z= 0.323 Chirality : 0.051 0.140 882 Planarity : 0.003 0.023 1116 Dihedral : 5.643 24.372 876 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 2.55 % Allowed : 17.72 % Favored : 79.73 % 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: -3.71 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 20 TYR 0.016 0.002 TYR D 86 PHE 0.017 0.001 PHE D 85 TRP 0.003 0.001 TRP B 3 HIS 0.008 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.11 ( 6276) covalent geometry : angle 0.60679 / 0.32 ( 8472) SS BOND : bond 0.00290 / 0.18 ( 18) SS BOND : angle 0.90078 / 0.64 ( 36) hydrogen bonds : bond 0.01575 / 1.04 ( 78) hydrogen bonds : angle 4.54754 / 3.10 ( 234) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.223 Fit side-chains REVERT: A 116 GLN cc_start: 0.8113 (mt0) cc_final: 0.7785 (mt0) REVERT: B 19 ASP cc_start: 0.7281 (OUTLIER) cc_final: 0.6934 (t70) REVERT: C 20 ARG cc_start: 0.8088 (mtt180) cc_final: 0.6877 (mmt-90) REVERT: C 33 ARG cc_start: 0.8769 (mmm160) cc_final: 0.6609 (mmt-90) REVERT: C 84 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7301 (ttm) REVERT: D 84 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7506 (tmm) REVERT: D 128 ASP cc_start: 0.8453 (m-30) cc_final: 0.7899 (p0) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.0715 time to fit residues: 8.8667 Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 8.9990 chunk 42 optimal weight: 0.0870 chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 29 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS A 29 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.129661 restraints weight = 7996.741| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 1.51 r_work: 0.3736 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6294 Z= 0.148 Angle : 0.637 5.329 8508 Z= 0.337 Chirality : 0.052 0.141 882 Planarity : 0.003 0.024 1116 Dihedral : 5.680 24.357 876 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 2.10 % Allowed : 17.87 % Favored : 80.03 % 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: -3.72 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 20 TYR 0.018 0.003 TYR E 86 PHE 0.017 0.001 PHE D 85 TRP 0.003 0.001 TRP C 3 HIS 0.009 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 6276) covalent geometry : angle 0.63557 / 0.34 ( 8472) SS BOND : bond 0.00328 / 0.20 ( 18) SS BOND : angle 0.94912 / 0.68 ( 36) hydrogen bonds : bond 0.01743 / 1.17 ( 78) hydrogen bonds : angle 4.52697 / 3.09 ( 234) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.145 Fit side-chains REVERT: A 84 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7604 (ttm) REVERT: B 19 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6945 (t70) REVERT: C 20 ARG cc_start: 0.8088 (mtt180) cc_final: 0.6889 (mmt-90) REVERT: C 33 ARG cc_start: 0.8789 (mmm160) cc_final: 0.6617 (mmt-90) REVERT: C 84 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.7237 (ttm) REVERT: D 84 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7340 (tmm) outliers start: 14 outliers final: 10 residues processed: 85 average time/residue: 0.0801 time to fit residues: 9.0910 Evaluate side-chains 94 residues out of total 666 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain B residue 19 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain C residue 43 SER Chi-restraints excluded: chain C residue 53 THR Chi-restraints excluded: chain C residue 84 MET Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain D residue 35 HIS Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain E residue 43 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 20.0000 chunk 69 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 HIS A 29 GLN A 116 GLN ** D 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 HIS ** E 65 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 = 0.3915 r_free = 0.3915 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.126827 restraints weight = 8032.449| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.51 r_work: 0.3690 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6294 Z= 0.201 Angle : 0.689 5.755 8508 Z= 0.366 Chirality : 0.053 0.143 882 Planarity : 0.003 0.028 1116 Dihedral : 5.885 26.366 876 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 2.70 % Allowed : 17.27 % Favored : 80.03 % 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: -3.79 (0.22), residues: 786 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.88 (0.17), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 20 TYR 0.020 0.003 TYR E 86 PHE 0.008 0.001 PHE E 85 TRP 0.004 0.001 TRP C 3 HIS 0.011 0.003 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 ( 6276) covalent geometry : angle 0.68694 / 0.37 ( 8472) SS BOND : bond 0.00404 / 0.24 ( 18) SS BOND : angle 1.06468 / 0.77 ( 36) hydrogen bonds : bond 0.02006 / 1.34 ( 78) hydrogen bonds : angle 4.58583 / 3.12 ( 234) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1481.51 seconds wall clock time: 26 minutes 10.21 seconds (1570.21 seconds total)