Starting phenix.real_space_refine on Sat May 2 06:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ufl_64111/05_2026/9ufl_64111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ufl_64111/05_2026/9ufl_64111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ufl_64111/05_2026/9ufl_64111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ufl_64111/05_2026/9ufl_64111.map" model { file = "/net/cci-nas-00/data/ceres_data/9ufl_64111/05_2026/9ufl_64111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ufl_64111/05_2026/9ufl_64111.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 1644 2.51 5 N 456 2.21 5 O 528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2628 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, D, F, A, B Time building chain proxies: 0.46, per 1000 atoms: 0.18 Number of scatterers: 2628 At special positions: 0 Unit cell: (108.73, 103.75, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 528 8.00 N 456 7.00 C 1644 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: 0.15 Conformation dependent library (CDL) restraints added in 93.5 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 68.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 38 through 41 removed outlier: 6.240A pdb=" N LEU E 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY C 41 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL E 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 66 removed outlier: 6.982A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL E 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA C 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR E 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA E 56 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU C 57 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS E 58 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C 59 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS E 45 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N VAL D 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY E 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N HIS D 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL E 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL D 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY E 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR D 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ALA E 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N ALA D 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N VAL E 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 9.957A pdb=" N LYS D 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N GLU E 57 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N LYS D 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR E 59 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N GLN D 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU E 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR D 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL E 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL D 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ASN E 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 82 removed outlier: 6.943A pdb=" N VAL E 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL C 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N THR E 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY C 73 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL C 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA E 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLN C 79 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS E 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR C 81 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL E 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N ALA E 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N THR D 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N VAL E 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N VAL D 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLY E 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA D 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR E 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA D 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.884A pdb=" N VAL E 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N LYS D 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N GLN E 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N VAL D 82 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N THR E 81 " --> pdb=" O VAL D 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 86 through 92 removed outlier: 6.581A pdb=" N GLY E 86 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ALA C 89 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE E 88 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA C 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA E 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA D 90 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA E 91 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR D 92 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 41 removed outlier: 6.239A pdb=" N LEU F 38 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N GLY A 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL F 40 " --> pdb=" O GLY A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 45 through 66 removed outlier: 6.983A pdb=" N GLU F 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N GLY A 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL F 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ALA A 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR F 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL A 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA F 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU A 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS F 58 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 59 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N LYS F 45 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N VAL B 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY F 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N HIS B 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL F 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N GLY F 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 10.090A pdb=" N THR B 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.963A pdb=" N ALA F 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N ALA B 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 9.144A pdb=" N VAL F 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.956A pdb=" N LYS B 58 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N GLU F 57 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 9.609A pdb=" N LYS B 60 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR F 59 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N GLN B 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU F 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N THR B 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL F 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL B 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ASN F 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.943A pdb=" N VAL F 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL A 71 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR F 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY A 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL A 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA F 78 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLN A 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N LYS F 80 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR A 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 82 " --> pdb=" O THR A 81 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA F 69 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N THR B 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 9.010A pdb=" N VAL F 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 9.123A pdb=" N VAL B 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY F 73 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N ALA B 76 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR F 75 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA B 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL F 77 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N LYS B 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N GLN F 79 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 10.410A pdb=" N VAL B 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N THR F 81 " --> pdb=" O VAL B 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 86 through 92 removed outlier: 6.580A pdb=" N GLY F 86 " --> pdb=" O SER A 87 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ALA A 89 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE F 88 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA A 91 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 9.147A pdb=" N ALA F 90 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA B 90 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ALA F 91 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 92 " --> pdb=" O ALA F 91 " (cutoff:3.500A) 40 hydrogen bonds defined for protein. 120 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: 0.27 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 462 1.29 - 1.35: 414 1.35 - 1.42: 102 1.42 - 1.48: 426 1.48 - 1.54: 1236 Bond restraints: 2640 Sorted by residual: bond pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " ideal model delta sigma weight residual 1.520 1.534 -0.014 3.00e-02 1.11e+03 2.12e-01 bond pdb=" CA LYS D 97 " pdb=" C LYS D 97 " ideal model delta sigma weight residual 1.527 1.533 -0.006 1.30e-02 5.92e+03 2.04e-01 bond pdb=" CB LYS A 97 " pdb=" CG LYS A 97 " ideal model delta sigma weight residual 1.520 1.534 -0.014 3.00e-02 1.11e+03 2.03e-01 bond pdb=" CA LYS F 97 " pdb=" C LYS F 97 " ideal model delta sigma weight residual 1.527 1.533 -0.006 1.30e-02 5.92e+03 2.02e-01 bond pdb=" CB LYS E 97 " pdb=" CG LYS E 97 " ideal model delta sigma weight residual 1.520 1.533 -0.013 3.00e-02 1.11e+03 1.93e-01 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.68: 3294 0.68 - 1.36: 222 1.36 - 2.03: 37 2.03 - 2.71: 5 2.71 - 3.39: 12 Bond angle restraints: 3570 Sorted by residual: angle pdb=" CG LYS A 97 " pdb=" CD LYS A 97 " pdb=" CE LYS A 97 " ideal model delta sigma weight residual 111.30 114.57 -3.27 2.30e+00 1.89e-01 2.02e+00 angle pdb=" CG LYS F 97 " pdb=" CD LYS F 97 " pdb=" CE LYS F 97 " ideal model delta sigma weight residual 111.30 114.54 -3.24 2.30e+00 1.89e-01 1.99e+00 angle pdb=" CG LYS E 97 " pdb=" CD LYS E 97 " pdb=" CE LYS E 97 " ideal model delta sigma weight residual 111.30 114.54 -3.24 2.30e+00 1.89e-01 1.98e+00 angle pdb=" CG LYS C 97 " pdb=" CD LYS C 97 " pdb=" CE LYS C 97 " ideal model delta sigma weight residual 111.30 114.53 -3.23 2.30e+00 1.89e-01 1.98e+00 angle pdb=" CG LYS B 97 " pdb=" CD LYS B 97 " pdb=" CE LYS B 97 " ideal model delta sigma weight residual 111.30 114.52 -3.22 2.30e+00 1.89e-01 1.96e+00 ... (remaining 3565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.07: 1320 14.07 - 28.14: 132 28.14 - 42.21: 78 42.21 - 56.28: 12 56.28 - 70.36: 6 Dihedral angle restraints: 1548 sinusoidal: 522 harmonic: 1026 Sorted by residual: dihedral pdb=" CA LEU E 38 " pdb=" CB LEU E 38 " pdb=" CG LEU E 38 " pdb=" CD1 LEU E 38 " ideal model delta sinusoidal sigma weight residual 180.00 134.02 45.98 3 1.50e+01 4.44e-03 8.26e+00 dihedral pdb=" CA LEU A 38 " pdb=" CB LEU A 38 " pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sinusoidal sigma weight residual 180.00 134.03 45.97 3 1.50e+01 4.44e-03 8.26e+00 dihedral pdb=" CA LEU B 38 " pdb=" CB LEU B 38 " pdb=" CG LEU B 38 " pdb=" CD1 LEU B 38 " ideal model delta sinusoidal sigma weight residual 180.00 134.03 45.97 3 1.50e+01 4.44e-03 8.26e+00 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 278 0.025 - 0.050: 90 0.050 - 0.075: 16 0.075 - 0.100: 15 0.100 - 0.125: 69 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.67e-01 ... (remaining 465 not shown) Planarity restraints: 444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.006 2.00e-02 2.50e+03 5.83e-03 5.94e-01 pdb=" CG PHE F 94 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 94 " -0.006 2.00e-02 2.50e+03 5.81e-03 5.91e-01 pdb=" CG PHE D 94 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE D 94 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 94 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 94 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 94 " -0.007 2.00e-02 2.50e+03 5.80e-03 5.90e-01 pdb=" CG PHE C 94 " 0.013 2.00e-02 2.50e+03 pdb=" CD1 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE C 94 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 94 " -0.002 2.00e-02 2.50e+03 ... (remaining 441 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1383 2.99 - 3.46: 2247 3.46 - 3.94: 3947 3.94 - 4.42: 4344 4.42 - 4.90: 9048 Nonbonded interactions: 20969 Sorted by model distance: nonbonded pdb=" O SER A 42 " pdb=" N THR A 44 " model vdw 2.507 3.120 nonbonded pdb=" O SER D 42 " pdb=" N THR D 44 " model vdw 2.508 3.120 nonbonded pdb=" O SER B 42 " pdb=" N THR B 44 " model vdw 2.508 3.120 nonbonded pdb=" O SER E 42 " pdb=" N THR E 44 " model vdw 2.508 3.120 nonbonded pdb=" O SER C 42 " pdb=" N THR C 44 " model vdw 2.508 3.120 ... (remaining 20964 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'A' selection = chain 'B' } 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: 4.370 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 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 : 0.002 0.014 2640 Z= 0.081 Angle : 0.419 3.389 3570 Z= 0.235 Chirality : 0.051 0.125 468 Planarity : 0.001 0.006 444 Dihedral : 15.948 70.355 900 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % 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: -1.56 (0.45), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR F 39 PHE 0.013 0.004 PHE F 94 HIS 0.003 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00153 ( 2640) covalent geometry : angle 0.41873 ( 3570) hydrogen bonds : bond 0.17799 ( 40) hydrogen bonds : angle 9.35748 ( 120) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.096 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.8688 time to fit residues: 59.0295 Evaluate side-chains 58 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 65 ASN E 79 GLN C 62 GLN C 65 ASN D 62 GLN D 65 ASN F 62 GLN F 65 ASN A 62 GLN A 65 ASN A 79 GLN B 65 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.137288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.098370 restraints weight = 2719.884| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.26 r_work: 0.3305 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8862 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 2640 Z= 0.262 Angle : 0.629 4.454 3570 Z= 0.353 Chirality : 0.054 0.141 468 Planarity : 0.003 0.009 444 Dihedral : 4.882 15.705 378 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 6.30 % Allowed : 18.52 % Favored : 75.19 % 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: -1.97 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR E 39 PHE 0.017 0.005 PHE E 94 HIS 0.007 0.004 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 2640) covalent geometry : angle 0.62871 ( 3570) hydrogen bonds : bond 0.03490 ( 40) hydrogen bonds : angle 6.55973 ( 120) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.099 Fit side-chains REVERT: E 60 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8196 (tptm) REVERT: D 39 TYR cc_start: 0.7720 (t80) cc_final: 0.7483 (t80) REVERT: D 60 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8504 (tttm) REVERT: F 60 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8400 (tttm) REVERT: A 60 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8552 (tptp) REVERT: A 61 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8161 (tt0) REVERT: B 39 TYR cc_start: 0.7541 (t80) cc_final: 0.7262 (t80) REVERT: B 61 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8349 (tt0) outliers start: 17 outliers final: 7 residues processed: 65 average time/residue: 0.7726 time to fit residues: 51.0415 Evaluate side-chains 70 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain F residue 60 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN C 62 GLN C 79 GLN F 62 GLN F 79 GLN A 62 GLN A 79 GLN B 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.140301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101059 restraints weight = 2711.682| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.30 r_work: 0.3337 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2640 Z= 0.170 Angle : 0.525 3.677 3570 Z= 0.297 Chirality : 0.053 0.141 468 Planarity : 0.002 0.008 444 Dihedral : 4.546 12.361 378 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 6.67 % Allowed : 18.52 % Favored : 74.81 % 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: -2.08 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 PHE 0.014 0.004 PHE E 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 2640) covalent geometry : angle 0.52512 ( 3570) hydrogen bonds : bond 0.02880 ( 40) hydrogen bonds : angle 6.35561 ( 120) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.098 Fit side-chains REVERT: C 60 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8475 (tptm) REVERT: D 39 TYR cc_start: 0.7715 (t80) cc_final: 0.7479 (t80) REVERT: D 60 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8448 (tttm) REVERT: F 57 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: A 61 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8165 (tt0) REVERT: B 39 TYR cc_start: 0.7540 (t80) cc_final: 0.7222 (t80) REVERT: B 61 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8321 (tt0) outliers start: 18 outliers final: 12 residues processed: 67 average time/residue: 0.7634 time to fit residues: 51.9642 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 43 LYS Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN C 62 GLN C 79 GLN F 62 GLN A 62 GLN A 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.135620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.097451 restraints weight = 2705.837| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.22 r_work: 0.3289 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.041 2640 Z= 0.362 Angle : 0.717 4.942 3570 Z= 0.402 Chirality : 0.058 0.147 468 Planarity : 0.003 0.009 444 Dihedral : 5.503 20.977 378 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 10.00 % Allowed : 18.52 % Favored : 71.48 % 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: -2.35 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.018 0.004 TYR F 39 PHE 0.020 0.005 PHE E 94 HIS 0.007 0.004 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00842 ( 2640) covalent geometry : angle 0.71750 ( 3570) hydrogen bonds : bond 0.04032 ( 40) hydrogen bonds : angle 6.43421 ( 120) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.104 Fit side-chains REVERT: E 60 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.8498 (tttm) REVERT: C 60 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8607 (tptp) REVERT: D 60 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8511 (tttm) REVERT: F 57 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: A 60 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8510 (tptm) REVERT: A 61 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: B 39 TYR cc_start: 0.7681 (t80) cc_final: 0.7346 (t80) REVERT: B 61 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8372 (tt0) outliers start: 27 outliers final: 11 residues processed: 69 average time/residue: 0.6687 time to fit residues: 46.9695 Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.0770 chunk 30 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN C 62 GLN F 62 GLN A 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.145844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.107333 restraints weight = 2680.457| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.27 r_work: 0.3458 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2640 Z= 0.076 Angle : 0.425 2.824 3570 Z= 0.240 Chirality : 0.052 0.130 468 Planarity : 0.001 0.007 444 Dihedral : 3.846 9.658 378 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 1.85 % Allowed : 27.78 % Favored : 70.37 % 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: -2.02 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.001 TYR A 39 PHE 0.008 0.002 PHE E 94 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00157 ( 2640) covalent geometry : angle 0.42507 ( 3570) hydrogen bonds : bond 0.01777 ( 40) hydrogen bonds : angle 6.02176 ( 120) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.099 Fit side-chains REVERT: C 60 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8335 (tptm) REVERT: C 97 LYS cc_start: 0.7425 (ttmm) cc_final: 0.6304 (mmpt) REVERT: A 62 GLN cc_start: 0.8614 (tt0) cc_final: 0.8409 (tt0) REVERT: B 61 GLU cc_start: 0.8602 (mt-10) cc_final: 0.8250 (tt0) outliers start: 5 outliers final: 1 residues processed: 66 average time/residue: 0.7569 time to fit residues: 50.7157 Evaluate side-chains 66 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain A residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 35 optimal weight: 10.0000 chunk 30 optimal weight: 0.0010 chunk 2 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 overall best weight: 3.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN C 62 GLN C 79 GLN D 62 GLN F 62 GLN F 79 GLN A 79 GLN B 62 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.137710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.098945 restraints weight = 2729.468| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.28 r_work: 0.3324 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2640 Z= 0.223 Angle : 0.562 3.699 3570 Z= 0.319 Chirality : 0.054 0.140 468 Planarity : 0.002 0.010 444 Dihedral : 4.815 13.332 378 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 5.19 % Allowed : 27.04 % Favored : 67.78 % 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: -2.19 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR E 39 PHE 0.016 0.004 PHE F 94 HIS 0.006 0.004 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 2640) covalent geometry : angle 0.56164 ( 3570) hydrogen bonds : bond 0.03059 ( 40) hydrogen bonds : angle 6.17974 ( 120) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.103 Fit side-chains REVERT: C 60 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8472 (tptm) REVERT: A 60 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8498 (tptp) REVERT: A 61 GLU cc_start: 0.8526 (tt0) cc_final: 0.8148 (tt0) REVERT: B 39 TYR cc_start: 0.7561 (t80) cc_final: 0.7299 (t80) REVERT: B 61 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8326 (tt0) outliers start: 14 outliers final: 9 residues processed: 68 average time/residue: 0.7122 time to fit residues: 49.2364 Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 60 LYS Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN C 62 GLN C 79 GLN F 62 GLN A 62 GLN A 79 GLN B 62 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.139189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.100586 restraints weight = 2711.898| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.26 r_work: 0.3352 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2640 Z= 0.157 Angle : 0.508 3.421 3570 Z= 0.288 Chirality : 0.053 0.141 468 Planarity : 0.002 0.008 444 Dihedral : 4.540 11.553 378 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 5.19 % Allowed : 27.41 % Favored : 67.41 % 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: -2.17 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR C 39 PHE 0.013 0.003 PHE E 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 2640) covalent geometry : angle 0.50768 ( 3570) hydrogen bonds : bond 0.02576 ( 40) hydrogen bonds : angle 6.16749 ( 120) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.114 Fit side-chains REVERT: C 60 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8408 (tptm) REVERT: F 57 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: A 61 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: B 39 TYR cc_start: 0.7507 (t80) cc_final: 0.7247 (t80) REVERT: B 61 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8327 (tt0) outliers start: 14 outliers final: 7 residues processed: 65 average time/residue: 0.7326 time to fit residues: 48.3504 Evaluate side-chains 68 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN C 62 GLN C 79 GLN D 79 GLN F 62 GLN F 79 GLN A 62 GLN A 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.138794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100097 restraints weight = 2781.409| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.28 r_work: 0.3344 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2640 Z= 0.167 Angle : 0.533 4.532 3570 Z= 0.299 Chirality : 0.053 0.140 468 Planarity : 0.002 0.009 444 Dihedral : 4.579 12.441 378 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 5.93 % Allowed : 25.93 % Favored : 68.15 % 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: -2.18 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR A 39 PHE 0.014 0.003 PHE E 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 2640) covalent geometry : angle 0.53332 ( 3570) hydrogen bonds : bond 0.02627 ( 40) hydrogen bonds : angle 6.16881 ( 120) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.137 Fit side-chains REVERT: C 60 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8413 (tptm) REVERT: C 97 LYS cc_start: 0.7572 (ttmm) cc_final: 0.6395 (mmpt) REVERT: D 60 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8483 (tttm) REVERT: F 57 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8263 (tt0) REVERT: A 61 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8148 (tt0) REVERT: A 97 LYS cc_start: 0.7518 (ttmm) cc_final: 0.6409 (mmpt) REVERT: B 39 TYR cc_start: 0.7496 (t80) cc_final: 0.7192 (t80) REVERT: B 61 GLU cc_start: 0.8679 (OUTLIER) cc_final: 0.8320 (tt0) outliers start: 16 outliers final: 8 residues processed: 65 average time/residue: 0.6706 time to fit residues: 44.3591 Evaluate side-chains 71 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN C 62 GLN C 79 GLN F 62 GLN A 62 GLN A 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.137934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099245 restraints weight = 2768.217| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.28 r_work: 0.3327 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2640 Z= 0.194 Angle : 0.555 4.007 3570 Z= 0.313 Chirality : 0.053 0.142 468 Planarity : 0.002 0.010 444 Dihedral : 4.774 13.172 378 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 6.67 % Allowed : 25.93 % Favored : 67.41 % 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: -2.22 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.002 TYR C 39 PHE 0.015 0.004 PHE E 94 HIS 0.006 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 2640) covalent geometry : angle 0.55546 ( 3570) hydrogen bonds : bond 0.02821 ( 40) hydrogen bonds : angle 6.20838 ( 120) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.075 Fit side-chains REVERT: C 60 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8486 (tptp) REVERT: C 97 LYS cc_start: 0.7536 (ttmm) cc_final: 0.6360 (mmpt) REVERT: D 60 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8497 (tttm) REVERT: F 57 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8259 (tt0) REVERT: A 61 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8153 (tt0) REVERT: A 97 LYS cc_start: 0.7549 (ttmm) cc_final: 0.6438 (mmpt) REVERT: B 39 TYR cc_start: 0.7511 (t80) cc_final: 0.7236 (t80) REVERT: B 61 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8335 (tt0) outliers start: 18 outliers final: 11 residues processed: 66 average time/residue: 0.6600 time to fit residues: 44.2761 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 21 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN C 62 GLN C 79 GLN F 62 GLN A 62 GLN A 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.137192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.098615 restraints weight = 2795.756| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.28 r_work: 0.3323 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2640 Z= 0.214 Angle : 0.578 3.787 3570 Z= 0.326 Chirality : 0.054 0.143 468 Planarity : 0.002 0.011 444 Dihedral : 4.903 14.314 378 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 7.04 % Allowed : 25.56 % Favored : 67.41 % 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: -2.29 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR A 39 PHE 0.016 0.004 PHE F 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 2640) covalent geometry : angle 0.57786 ( 3570) hydrogen bonds : bond 0.02972 ( 40) hydrogen bonds : angle 6.24172 ( 120) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.061 Fit side-chains REVERT: C 60 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8519 (tptp) REVERT: C 97 LYS cc_start: 0.7491 (ttmm) cc_final: 0.6326 (mmpt) REVERT: D 60 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8484 (tttm) REVERT: F 57 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: A 61 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8167 (tt0) REVERT: A 97 LYS cc_start: 0.7554 (ttmm) cc_final: 0.6427 (mmpt) REVERT: B 39 TYR cc_start: 0.7527 (t80) cc_final: 0.7281 (t80) REVERT: B 61 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8366 (tt0) outliers start: 19 outliers final: 10 residues processed: 68 average time/residue: 0.6756 time to fit residues: 46.7129 Evaluate side-chains 74 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 60 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 60 LYS Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 57 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 61 GLU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 13 optimal weight: 0.0010 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN E 79 GLN C 62 GLN C 79 GLN F 62 GLN A 62 GLN A 79 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.137649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.099136 restraints weight = 2790.068| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.29 r_work: 0.3329 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2640 Z= 0.194 Angle : 0.556 3.638 3570 Z= 0.314 Chirality : 0.053 0.142 468 Planarity : 0.002 0.011 444 Dihedral : 4.801 13.528 378 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 6.67 % Allowed : 26.30 % Favored : 67.04 % 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: -2.24 (0.42), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.002 TYR C 39 PHE 0.015 0.004 PHE F 94 HIS 0.006 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 2640) covalent geometry : angle 0.55610 ( 3570) hydrogen bonds : bond 0.02824 ( 40) hydrogen bonds : angle 6.23951 ( 120) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1440.08 seconds wall clock time: 25 minutes 16.72 seconds (1516.72 seconds total)