Starting phenix.real_space_refine on Tue Mar 3 12:13:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6osl_20185/03_2026/6osl_20185.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osl_20185/03_2026/6osl_20185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2026/6osl_20185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2026/6osl_20185.map" model { file = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2026/6osl_20185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2026/6osl_20185.cif" } resolution = 3.0 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= 0.008 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 2540 2.51 5 N 710 2.21 5 O 810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 406 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.51, per 1000 atoms: 0.13 Number of scatterers: 4060 At special positions: 0 Unit cell: (98.58, 83.74, 42.4, 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 810 8.00 N 710 7.00 C 2540 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: 0.23 Conformation dependent library (CDL) restraints added in 175.0 milliseconds 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1000 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 49.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 41 removed outlier: 6.706A pdb=" N VAL A 40 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL E 40 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL G 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 7.313A pdb=" N GLU C 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY A 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU E 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLY C 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU E 46 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL G 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.311A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLU I 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY G 47 " --> pdb=" O GLU I 46 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.527A pdb=" N VAL E 52 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N VAL G 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 65 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 75 removed outlier: 9.171A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA G 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR E 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS C 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 75 removed outlier: 9.171A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 10.579A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N VAL E 74 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY C 73 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 8.952A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 10.419A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 9.310A pdb=" N VAL G 74 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY E 73 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ALA G 76 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 10.417A pdb=" N THR I 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 9.047A pdb=" N VAL G 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) removed outlier: 9.293A pdb=" N VAL I 74 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLY G 73 " --> pdb=" O VAL I 74 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA I 76 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 8.645A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N LYS I 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N GLN G 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AA8, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 8.313A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 9.207A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU F 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N GLY D 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N GLU F 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N VAL H 49 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU J 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY H 47 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 52 through 57 removed outlier: 6.498A pdb=" N VAL B 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N GLU D 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA B 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL F 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL H 55 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR F 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLU H 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA F 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 62 through 65 Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 75 removed outlier: 8.967A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 10.432A pdb=" N THR D 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 9.064A pdb=" N VAL B 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 9.307A pdb=" N VAL D 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLY B 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 10.385A pdb=" N THR F 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL D 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N VAL F 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLY D 73 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 10.388A pdb=" N THR H 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N VAL F 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL H 74 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLY F 73 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ALA H 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N THR J 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N VAL H 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N VAL J 74 " --> pdb=" O VAL H 71 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY H 73 " --> pdb=" O VAL J 74 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 78 through 81 removed outlier: 6.809A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA F 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR H 81 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS F 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ALA H 78 " --> pdb=" O GLN J 79 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR J 81 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LYS H 80 " --> pdb=" O THR J 81 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 86 through 88 Processing sheet with id=AB6, first strand: chain 'B' and resid 91 through 92 Processing sheet with id=AB7, first strand: chain 'D' and resid 40 through 41 removed outlier: 6.522A pdb=" N VAL D 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL F 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL H 40 " --> pdb=" O GLY J 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 95 hydrogen bonds defined for protein. 279 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: 0.53 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 700 1.28 - 1.35: 630 1.35 - 1.42: 180 1.42 - 1.48: 701 1.48 - 1.55: 1869 Bond restraints: 4080 Sorted by residual: bond pdb=" CB GLU I 57 " pdb=" CG GLU I 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" CB GLU H 57 " pdb=" CG GLU H 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLU D 57 " pdb=" CG GLU D 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.18e+00 bond pdb=" CB GLU C 57 " pdb=" CG GLU C 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.16e+00 bond pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.14e+00 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 5188 1.84 - 3.69: 260 3.69 - 5.53: 42 5.53 - 7.37: 0 7.37 - 9.22: 20 Bond angle restraints: 5510 Sorted by residual: angle pdb=" C VAL J 49 " pdb=" N HIS J 50 " pdb=" CA HIS J 50 " ideal model delta sigma weight residual 122.46 113.24 9.22 1.80e+00 3.09e-01 2.62e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.61e+01 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 122.46 113.27 9.19 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C VAL I 49 " pdb=" N HIS I 50 " pdb=" CA HIS I 50 " ideal model delta sigma weight residual 122.46 113.28 9.18 1.80e+00 3.09e-01 2.60e+01 ... (remaining 5505 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 16.33: 2200 16.33 - 32.65: 159 32.65 - 48.97: 11 48.97 - 65.29: 0 65.29 - 81.62: 10 Dihedral angle restraints: 2380 sinusoidal: 790 harmonic: 1590 Sorted by residual: dihedral pdb=" CA THR D 75 " pdb=" C THR D 75 " pdb=" N ALA D 76 " pdb=" CA ALA D 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA THR J 75 " pdb=" C THR J 75 " pdb=" N ALA J 76 " pdb=" CA ALA J 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 dihedral pdb=" CA THR G 75 " pdb=" C THR G 75 " pdb=" N ALA G 76 " pdb=" CA ALA G 76 " ideal model delta harmonic sigma weight residual 180.00 164.48 15.52 0 5.00e+00 4.00e-02 9.63e+00 ... (remaining 2377 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 490 0.062 - 0.123: 187 0.123 - 0.185: 33 0.185 - 0.246: 0 0.246 - 0.308: 10 Chirality restraints: 720 Sorted by residual: chirality pdb=" CA HIS A 50 " pdb=" N HIS A 50 " pdb=" C HIS A 50 " pdb=" CB HIS A 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA HIS B 50 " pdb=" N HIS B 50 " pdb=" C HIS B 50 " pdb=" CB HIS B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA HIS E 50 " pdb=" N HIS E 50 " pdb=" C HIS E 50 " pdb=" CB HIS E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 717 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS H 50 " 0.020 2.00e-02 2.50e+03 1.81e-02 4.90e+00 pdb=" CG HIS H 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS H 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS H 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS H 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS H 50 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 50 " 0.020 2.00e-02 2.50e+03 1.79e-02 4.82e+00 pdb=" CG HIS F 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS F 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS F 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS F 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS F 50 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.019 2.00e-02 2.50e+03 1.79e-02 4.80e+00 pdb=" CG HIS B 50 " -0.038 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.006 2.00e-02 2.50e+03 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1390 2.83 - 3.34: 3595 3.34 - 3.86: 6312 3.86 - 4.38: 6929 4.38 - 4.90: 14282 Nonbonded interactions: 32508 Sorted by model distance: nonbonded pdb=" O HIS B 50 " pdb=" O GLY D 51 " model vdw 2.308 3.040 nonbonded pdb=" O HIS E 50 " pdb=" O GLY G 51 " model vdw 2.367 3.040 nonbonded pdb=" O HIS F 50 " pdb=" O GLY H 51 " model vdw 2.385 3.040 nonbonded pdb=" O HIS C 50 " pdb=" O GLY E 51 " model vdw 2.392 3.040 nonbonded pdb=" O HIS G 50 " pdb=" O GLY I 51 " model vdw 2.397 3.040 ... (remaining 32503 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.010 Set scattering table: 0.020 Process input model: 5.370 Find NCS groups from input model: 0.040 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:8.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 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 : 0.010 0.044 4080 Z= 0.465 Angle : 1.064 9.216 5510 Z= 0.629 Chirality : 0.074 0.308 720 Planarity : 0.004 0.018 680 Dihedral : 13.469 81.616 1380 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 2.44 % Allowed : 16.83 % Favored : 80.73 % 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: -4.40 (0.22), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR H 39 PHE 0.003 0.001 PHE B 94 HIS 0.016 0.010 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.01043 ( 4080) covalent geometry : angle 1.06368 ( 5510) hydrogen bonds : bond 0.23085 ( 95) hydrogen bonds : angle 8.61433 ( 279) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.160 Fit side-chains REVERT: A 57 GLU cc_start: 0.8300 (pt0) cc_final: 0.8061 (pt0) REVERT: B 57 GLU cc_start: 0.8476 (pt0) cc_final: 0.8251 (pt0) REVERT: B 60 LYS cc_start: 0.8175 (mttt) cc_final: 0.7827 (mtpt) REVERT: B 94 PHE cc_start: 0.7459 (p90) cc_final: 0.6872 (p90) REVERT: B 96 LYS cc_start: 0.6521 (ttmt) cc_final: 0.5825 (tttm) REVERT: C 45 LYS cc_start: 0.7281 (pttt) cc_final: 0.6868 (ptmt) REVERT: C 57 GLU cc_start: 0.8071 (pt0) cc_final: 0.7845 (pt0) REVERT: C 60 LYS cc_start: 0.8111 (mttt) cc_final: 0.7853 (mttp) REVERT: C 94 PHE cc_start: 0.7878 (p90) cc_final: 0.7667 (p90) REVERT: C 96 LYS cc_start: 0.6006 (ttmt) cc_final: 0.5290 (tttm) REVERT: D 45 LYS cc_start: 0.7180 (pttt) cc_final: 0.6720 (ptpt) REVERT: D 60 LYS cc_start: 0.8216 (mttt) cc_final: 0.7880 (mttp) REVERT: D 96 LYS cc_start: 0.5686 (ttmt) cc_final: 0.5187 (tttm) REVERT: E 60 LYS cc_start: 0.8442 (mttt) cc_final: 0.7882 (mtpt) REVERT: E 94 PHE cc_start: 0.7846 (p90) cc_final: 0.7544 (p90) REVERT: E 96 LYS cc_start: 0.5450 (ttmt) cc_final: 0.4832 (tttp) REVERT: F 60 LYS cc_start: 0.8252 (mttt) cc_final: 0.7744 (mtpt) REVERT: F 94 PHE cc_start: 0.7570 (p90) cc_final: 0.7072 (p90) REVERT: F 96 LYS cc_start: 0.5874 (ttmt) cc_final: 0.5444 (tttp) REVERT: G 96 LYS cc_start: 0.4790 (ttmt) cc_final: 0.4355 (tttm) REVERT: H 60 LYS cc_start: 0.7935 (mttt) cc_final: 0.7581 (mttp) REVERT: H 96 LYS cc_start: 0.4792 (ttmt) cc_final: 0.4339 (tttm) REVERT: I 60 LYS cc_start: 0.8096 (mttt) cc_final: 0.7402 (tttm) REVERT: I 94 PHE cc_start: 0.7633 (p90) cc_final: 0.5078 (m-80) REVERT: I 96 LYS cc_start: 0.5840 (ttmt) cc_final: 0.5302 (tttp) REVERT: J 60 LYS cc_start: 0.7840 (mttt) cc_final: 0.7307 (tttm) REVERT: J 94 PHE cc_start: 0.7679 (p90) cc_final: 0.5194 (t80) REVERT: J 96 LYS cc_start: 0.5533 (ttmt) cc_final: 0.5071 (tttm) outliers start: 10 outliers final: 0 residues processed: 96 average time/residue: 0.5683 time to fit residues: 56.1286 Evaluate side-chains 68 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 8.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.216069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.187489 restraints weight = 4286.141| |-----------------------------------------------------------------------------| r_work (start): 0.4550 rms_B_bonded: 2.64 r_work: 0.4437 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4318 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4080 Z= 0.142 Angle : 0.665 7.285 5510 Z= 0.396 Chirality : 0.058 0.219 720 Planarity : 0.003 0.017 680 Dihedral : 5.148 13.582 590 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 7.07 % Allowed : 18.05 % Favored : 74.88 % 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: -3.87 (0.25), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.19), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR G 39 PHE 0.007 0.002 PHE F 94 HIS 0.014 0.007 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4080) covalent geometry : angle 0.66474 ( 5510) hydrogen bonds : bond 0.02658 ( 95) hydrogen bonds : angle 6.17220 ( 279) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.152 Fit side-chains REVERT: A 57 GLU cc_start: 0.8451 (pt0) cc_final: 0.8025 (pt0) REVERT: A 60 LYS cc_start: 0.8664 (mttt) cc_final: 0.8212 (mttp) REVERT: A 96 LYS cc_start: 0.5843 (ttmt) cc_final: 0.5202 (tttm) REVERT: B 45 LYS cc_start: 0.6741 (pttt) cc_final: 0.6382 (ptpt) REVERT: B 60 LYS cc_start: 0.8490 (mttt) cc_final: 0.8025 (mtpt) REVERT: B 96 LYS cc_start: 0.6252 (ttmt) cc_final: 0.5549 (tttm) REVERT: C 45 LYS cc_start: 0.6739 (pttt) cc_final: 0.6388 (ptmt) REVERT: C 60 LYS cc_start: 0.8310 (mttt) cc_final: 0.8023 (mttm) REVERT: C 94 PHE cc_start: 0.7913 (p90) cc_final: 0.7664 (p90) REVERT: C 96 LYS cc_start: 0.5494 (ttmt) cc_final: 0.4811 (tttm) REVERT: D 45 LYS cc_start: 0.6987 (pttt) cc_final: 0.6679 (ptpt) REVERT: D 60 LYS cc_start: 0.8447 (mttt) cc_final: 0.7989 (mttp) REVERT: D 94 PHE cc_start: 0.7853 (p90) cc_final: 0.7247 (p90) REVERT: D 96 LYS cc_start: 0.5101 (ttmt) cc_final: 0.4518 (tttm) REVERT: E 57 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: E 60 LYS cc_start: 0.8478 (mttt) cc_final: 0.7872 (mtpt) REVERT: E 94 PHE cc_start: 0.7865 (p90) cc_final: 0.7474 (p90) REVERT: E 96 LYS cc_start: 0.4791 (ttmt) cc_final: 0.4087 (tttp) REVERT: F 60 LYS cc_start: 0.8316 (mttt) cc_final: 0.7769 (mtpt) REVERT: F 94 PHE cc_start: 0.7714 (p90) cc_final: 0.7269 (p90) REVERT: F 96 LYS cc_start: 0.5305 (ttmt) cc_final: 0.4663 (tttp) REVERT: G 60 LYS cc_start: 0.8118 (mttt) cc_final: 0.7816 (mttp) REVERT: G 96 LYS cc_start: 0.4252 (ttmt) cc_final: 0.3835 (tttm) REVERT: H 60 LYS cc_start: 0.8026 (mttt) cc_final: 0.7548 (mttp) REVERT: H 96 LYS cc_start: 0.4826 (ttmt) cc_final: 0.4427 (tttp) REVERT: I 60 LYS cc_start: 0.8196 (mttt) cc_final: 0.7401 (tttm) REVERT: I 94 PHE cc_start: 0.7769 (p90) cc_final: 0.5159 (m-80) REVERT: I 96 LYS cc_start: 0.5247 (ttmt) cc_final: 0.4699 (tttp) REVERT: J 60 LYS cc_start: 0.8060 (mttt) cc_final: 0.7277 (tttm) REVERT: J 94 PHE cc_start: 0.8016 (p90) cc_final: 0.5363 (t80) REVERT: J 96 LYS cc_start: 0.4884 (ttmt) cc_final: 0.4453 (tttm) outliers start: 29 outliers final: 13 residues processed: 93 average time/residue: 0.5167 time to fit residues: 49.7100 Evaluate side-chains 85 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 48 optimal weight: 0.0000 chunk 40 optimal weight: 8.9990 overall best weight: 4.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.203740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.174197 restraints weight = 4417.176| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.58 r_work: 0.4334 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4080 Z= 0.240 Angle : 0.781 8.606 5510 Z= 0.463 Chirality : 0.061 0.277 720 Planarity : 0.003 0.018 680 Dihedral : 5.594 15.792 590 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 10.00 % Allowed : 16.10 % Favored : 73.90 % 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: -3.73 (0.25), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.19), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.016 0.002 PHE A 94 HIS 0.017 0.009 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 4080) covalent geometry : angle 0.78119 ( 5510) hydrogen bonds : bond 0.03085 ( 95) hydrogen bonds : angle 6.21726 ( 279) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 69 time to evaluate : 0.098 Fit side-chains REVERT: A 57 GLU cc_start: 0.8401 (pt0) cc_final: 0.8140 (pt0) REVERT: A 60 LYS cc_start: 0.8653 (mttt) cc_final: 0.8190 (mttp) REVERT: A 96 LYS cc_start: 0.6203 (ttmt) cc_final: 0.5563 (tttp) REVERT: B 45 LYS cc_start: 0.7235 (pttt) cc_final: 0.6875 (ptpt) REVERT: B 60 LYS cc_start: 0.8380 (mttt) cc_final: 0.7925 (mtpt) REVERT: B 96 LYS cc_start: 0.6355 (ttmt) cc_final: 0.5634 (tttm) REVERT: C 45 LYS cc_start: 0.6765 (pttt) cc_final: 0.6362 (ptmt) REVERT: C 60 LYS cc_start: 0.8262 (mttt) cc_final: 0.7947 (mttm) REVERT: C 94 PHE cc_start: 0.7939 (p90) cc_final: 0.7708 (p90) REVERT: C 96 LYS cc_start: 0.5647 (ttmt) cc_final: 0.5009 (tttm) REVERT: D 60 LYS cc_start: 0.8348 (mttt) cc_final: 0.7987 (mttp) REVERT: D 94 PHE cc_start: 0.7817 (p90) cc_final: 0.7399 (p90) REVERT: D 96 LYS cc_start: 0.5244 (ttmt) cc_final: 0.4697 (tttm) REVERT: E 57 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8447 (pt0) REVERT: E 60 LYS cc_start: 0.8378 (mttt) cc_final: 0.7763 (mtpt) REVERT: E 94 PHE cc_start: 0.7907 (p90) cc_final: 0.7556 (p90) REVERT: E 96 LYS cc_start: 0.5030 (ttmt) cc_final: 0.4314 (tttp) REVERT: F 60 LYS cc_start: 0.8300 (mttt) cc_final: 0.7724 (mtpt) REVERT: F 94 PHE cc_start: 0.7828 (p90) cc_final: 0.7452 (p90) REVERT: F 96 LYS cc_start: 0.5356 (ttmt) cc_final: 0.4714 (tttp) REVERT: G 96 LYS cc_start: 0.4436 (ttmt) cc_final: 0.4008 (tttm) REVERT: H 60 LYS cc_start: 0.8025 (mttt) cc_final: 0.7510 (mttp) REVERT: H 96 LYS cc_start: 0.4890 (ttmt) cc_final: 0.4401 (tttm) REVERT: I 60 LYS cc_start: 0.8247 (mttt) cc_final: 0.7444 (tttm) REVERT: I 94 PHE cc_start: 0.7906 (p90) cc_final: 0.5174 (m-80) REVERT: I 96 LYS cc_start: 0.5196 (ttmt) cc_final: 0.4588 (tttp) REVERT: J 60 LYS cc_start: 0.8051 (mttt) cc_final: 0.7349 (tttm) REVERT: J 94 PHE cc_start: 0.7802 (p90) cc_final: 0.5360 (t80) REVERT: J 96 LYS cc_start: 0.4895 (ttmt) cc_final: 0.4434 (tttm) outliers start: 41 outliers final: 33 residues processed: 90 average time/residue: 0.5060 time to fit residues: 47.0136 Evaluate side-chains 101 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.218361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.189159 restraints weight = 4279.669| |-----------------------------------------------------------------------------| r_work (start): 0.4589 rms_B_bonded: 2.61 r_work: 0.4495 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.4381 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4080 Z= 0.112 Angle : 0.585 6.216 5510 Z= 0.350 Chirality : 0.055 0.215 720 Planarity : 0.003 0.017 680 Dihedral : 4.730 16.272 590 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 8.29 % Allowed : 18.05 % Favored : 73.66 % 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: -3.41 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.015 0.002 PHE A 94 HIS 0.013 0.006 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 4080) covalent geometry : angle 0.58510 ( 5510) hydrogen bonds : bond 0.02041 ( 95) hydrogen bonds : angle 5.61870 ( 279) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 0.157 Fit side-chains REVERT: A 57 GLU cc_start: 0.8386 (pt0) cc_final: 0.7946 (pt0) REVERT: A 60 LYS cc_start: 0.8528 (mttt) cc_final: 0.8107 (mttp) REVERT: A 96 LYS cc_start: 0.6590 (ttmt) cc_final: 0.5933 (tttp) REVERT: B 60 LYS cc_start: 0.8409 (mttt) cc_final: 0.7924 (mtpt) REVERT: B 96 LYS cc_start: 0.6487 (ttmt) cc_final: 0.5743 (tttm) REVERT: C 45 LYS cc_start: 0.6798 (pttt) cc_final: 0.6419 (ptmt) REVERT: C 60 LYS cc_start: 0.8278 (mttt) cc_final: 0.7995 (mttp) REVERT: C 96 LYS cc_start: 0.5796 (ttmt) cc_final: 0.5192 (tttm) REVERT: D 60 LYS cc_start: 0.8372 (mttt) cc_final: 0.7981 (mttp) REVERT: D 94 PHE cc_start: 0.7922 (p90) cc_final: 0.7537 (p90) REVERT: D 96 LYS cc_start: 0.5356 (ttmt) cc_final: 0.4787 (tttm) REVERT: E 49 VAL cc_start: 0.9016 (OUTLIER) cc_final: 0.8791 (p) REVERT: E 60 LYS cc_start: 0.8378 (mttt) cc_final: 0.7839 (mtpt) REVERT: E 94 PHE cc_start: 0.7768 (p90) cc_final: 0.7417 (p90) REVERT: E 96 LYS cc_start: 0.5228 (ttmt) cc_final: 0.4430 (tttp) REVERT: F 45 LYS cc_start: 0.7333 (OUTLIER) cc_final: 0.6814 (ptpt) REVERT: F 60 LYS cc_start: 0.8302 (mttt) cc_final: 0.7789 (mtpt) REVERT: F 94 PHE cc_start: 0.7820 (p90) cc_final: 0.7520 (p90) REVERT: F 96 LYS cc_start: 0.5467 (ttmt) cc_final: 0.4805 (tttp) REVERT: G 96 LYS cc_start: 0.4419 (ttmt) cc_final: 0.3974 (tttm) REVERT: H 60 LYS cc_start: 0.7973 (mttt) cc_final: 0.7545 (mttp) REVERT: H 96 LYS cc_start: 0.4854 (ttmt) cc_final: 0.4403 (tttp) REVERT: I 60 LYS cc_start: 0.8151 (mttt) cc_final: 0.7473 (tttp) REVERT: I 94 PHE cc_start: 0.7849 (p90) cc_final: 0.5203 (m-80) REVERT: I 96 LYS cc_start: 0.5315 (ttmt) cc_final: 0.4675 (tttp) REVERT: J 60 LYS cc_start: 0.8041 (mttt) cc_final: 0.7385 (tttm) REVERT: J 94 PHE cc_start: 0.7898 (p90) cc_final: 0.5398 (t80) REVERT: J 96 LYS cc_start: 0.5045 (ttmt) cc_final: 0.4526 (tttm) outliers start: 34 outliers final: 23 residues processed: 97 average time/residue: 0.4737 time to fit residues: 47.5925 Evaluate side-chains 101 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 36 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 20.0000 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 8.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.210112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.180806 restraints weight = 4332.103| |-----------------------------------------------------------------------------| r_work (start): 0.4503 rms_B_bonded: 2.59 r_work: 0.4414 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4302 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4080 Z= 0.171 Angle : 0.678 7.418 5510 Z= 0.403 Chirality : 0.057 0.250 720 Planarity : 0.003 0.021 680 Dihedral : 5.110 16.516 590 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 11.22 % Allowed : 14.39 % Favored : 74.39 % 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: -3.34 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR C 39 PHE 0.018 0.002 PHE C 94 HIS 0.014 0.007 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4080) covalent geometry : angle 0.67810 ( 5510) hydrogen bonds : bond 0.02454 ( 95) hydrogen bonds : angle 5.82139 ( 279) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 72 time to evaluate : 0.192 Fit side-chains REVERT: A 60 LYS cc_start: 0.8610 (mttt) cc_final: 0.8171 (mttp) REVERT: A 96 LYS cc_start: 0.6529 (ttmt) cc_final: 0.5849 (tttp) REVERT: B 60 LYS cc_start: 0.8357 (mttt) cc_final: 0.7927 (mtpt) REVERT: B 96 LYS cc_start: 0.6569 (ttmt) cc_final: 0.5813 (tttm) REVERT: C 60 LYS cc_start: 0.8265 (mttt) cc_final: 0.7968 (mttm) REVERT: C 96 LYS cc_start: 0.5594 (ttmt) cc_final: 0.5208 (tttm) REVERT: D 60 LYS cc_start: 0.8308 (mttt) cc_final: 0.7898 (mttp) REVERT: D 94 PHE cc_start: 0.7725 (p90) cc_final: 0.7377 (p90) REVERT: D 96 LYS cc_start: 0.5302 (ttmt) cc_final: 0.4748 (tttm) REVERT: E 46 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7562 (mt-10) REVERT: E 57 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8487 (pt0) REVERT: E 60 LYS cc_start: 0.8360 (mttt) cc_final: 0.7783 (mtpt) REVERT: E 94 PHE cc_start: 0.7855 (p90) cc_final: 0.7493 (p90) REVERT: E 96 LYS cc_start: 0.5124 (ttmt) cc_final: 0.4356 (tttp) REVERT: F 45 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6868 (ptpt) REVERT: F 46 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7504 (mt-10) REVERT: F 60 LYS cc_start: 0.8310 (mttt) cc_final: 0.7761 (mtpt) REVERT: F 94 PHE cc_start: 0.7945 (p90) cc_final: 0.7651 (p90) REVERT: F 96 LYS cc_start: 0.5481 (ttmt) cc_final: 0.4865 (tttp) REVERT: G 96 LYS cc_start: 0.4374 (ttmt) cc_final: 0.3936 (tttm) REVERT: H 60 LYS cc_start: 0.7939 (mttt) cc_final: 0.7510 (mttp) REVERT: H 96 LYS cc_start: 0.4850 (ttmt) cc_final: 0.4407 (tttp) REVERT: I 60 LYS cc_start: 0.8213 (mttt) cc_final: 0.7485 (tttm) REVERT: I 94 PHE cc_start: 0.7884 (p90) cc_final: 0.5179 (m-80) REVERT: I 96 LYS cc_start: 0.5199 (ttmt) cc_final: 0.4601 (tttp) REVERT: J 60 LYS cc_start: 0.8025 (mttt) cc_final: 0.7369 (tttp) REVERT: J 94 PHE cc_start: 0.7806 (p90) cc_final: 0.5329 (t80) REVERT: J 96 LYS cc_start: 0.4952 (ttmt) cc_final: 0.4358 (tmtm) outliers start: 46 outliers final: 40 residues processed: 97 average time/residue: 0.4534 time to fit residues: 45.6481 Evaluate side-chains 112 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 69 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 15 optimal weight: 30.0000 chunk 39 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.203067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.173149 restraints weight = 4490.224| |-----------------------------------------------------------------------------| r_work (start): 0.4424 rms_B_bonded: 2.63 r_work: 0.4334 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4080 Z= 0.257 Angle : 0.789 8.985 5510 Z= 0.466 Chirality : 0.061 0.282 720 Planarity : 0.003 0.021 680 Dihedral : 5.623 15.187 590 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 12.20 % Allowed : 14.15 % Favored : 73.66 % 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: -3.50 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.001 TYR A 39 PHE 0.010 0.001 PHE C 94 HIS 0.015 0.008 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00582 ( 4080) covalent geometry : angle 0.78862 ( 5510) hydrogen bonds : bond 0.02913 ( 95) hydrogen bonds : angle 6.10799 ( 279) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 66 time to evaluate : 0.149 Fit side-chains REVERT: A 60 LYS cc_start: 0.8642 (mttt) cc_final: 0.8189 (mttp) REVERT: A 96 LYS cc_start: 0.6492 (ttmt) cc_final: 0.5833 (tttp) REVERT: B 60 LYS cc_start: 0.8399 (mttt) cc_final: 0.7934 (mtpt) REVERT: B 96 LYS cc_start: 0.6406 (ttmt) cc_final: 0.5693 (tttm) REVERT: C 60 LYS cc_start: 0.8269 (mttt) cc_final: 0.7949 (mttm) REVERT: C 96 LYS cc_start: 0.5542 (ttmt) cc_final: 0.5197 (tttm) REVERT: D 60 LYS cc_start: 0.8331 (mttt) cc_final: 0.7905 (mttp) REVERT: D 96 LYS cc_start: 0.5226 (ttmt) cc_final: 0.4743 (tttm) REVERT: E 60 LYS cc_start: 0.8356 (mttt) cc_final: 0.7767 (mtpt) REVERT: E 96 LYS cc_start: 0.5083 (ttmt) cc_final: 0.4454 (tttp) REVERT: F 45 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6901 (ptpt) REVERT: F 46 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: F 60 LYS cc_start: 0.8299 (mttt) cc_final: 0.7729 (mtpt) REVERT: F 94 PHE cc_start: 0.7797 (p90) cc_final: 0.7516 (p90) REVERT: F 96 LYS cc_start: 0.5232 (ttmt) cc_final: 0.4603 (tttp) REVERT: G 96 LYS cc_start: 0.4318 (ttmt) cc_final: 0.3886 (tttm) REVERT: H 60 LYS cc_start: 0.7979 (mttt) cc_final: 0.7507 (mttp) REVERT: H 96 LYS cc_start: 0.4869 (ttmt) cc_final: 0.4388 (tttp) REVERT: I 60 LYS cc_start: 0.8244 (mttt) cc_final: 0.7453 (tttm) REVERT: I 94 PHE cc_start: 0.7936 (p90) cc_final: 0.5115 (m-80) REVERT: I 96 LYS cc_start: 0.5115 (ttmt) cc_final: 0.4513 (tttp) REVERT: J 60 LYS cc_start: 0.8073 (mttt) cc_final: 0.7314 (tttm) REVERT: J 94 PHE cc_start: 0.7742 (p90) cc_final: 0.5326 (t80) REVERT: J 96 LYS cc_start: 0.4800 (ttmt) cc_final: 0.4287 (tmtm) outliers start: 50 outliers final: 41 residues processed: 97 average time/residue: 0.4377 time to fit residues: 44.1341 Evaluate side-chains 107 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 35 optimal weight: 20.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4704 r_free = 0.4704 target = 0.206724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.177314 restraints weight = 4474.994| |-----------------------------------------------------------------------------| r_work (start): 0.4460 rms_B_bonded: 2.57 r_work: 0.4367 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4256 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4080 Z= 0.212 Angle : 0.730 8.344 5510 Z= 0.432 Chirality : 0.059 0.264 720 Planarity : 0.003 0.019 680 Dihedral : 5.404 15.706 590 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 12.20 % Allowed : 14.39 % Favored : 73.41 % 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: -3.43 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 PHE 0.013 0.002 PHE D 94 HIS 0.015 0.008 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 4080) covalent geometry : angle 0.72994 ( 5510) hydrogen bonds : bond 0.02678 ( 95) hydrogen bonds : angle 6.00794 ( 279) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 67 time to evaluate : 0.149 Fit side-chains REVERT: A 60 LYS cc_start: 0.8636 (mttt) cc_final: 0.8198 (mttp) REVERT: A 96 LYS cc_start: 0.6547 (ttmt) cc_final: 0.5886 (tttp) REVERT: B 45 LYS cc_start: 0.7201 (pttt) cc_final: 0.6993 (ptpt) REVERT: B 60 LYS cc_start: 0.8392 (mttt) cc_final: 0.7966 (mtpt) REVERT: B 96 LYS cc_start: 0.6459 (ttmt) cc_final: 0.5719 (tttm) REVERT: C 60 LYS cc_start: 0.8268 (mttt) cc_final: 0.7964 (mttm) REVERT: C 96 LYS cc_start: 0.5595 (ttmt) cc_final: 0.5249 (tttm) REVERT: D 60 LYS cc_start: 0.8346 (mttt) cc_final: 0.7930 (mttp) REVERT: D 94 PHE cc_start: 0.7707 (p90) cc_final: 0.7334 (p90) REVERT: D 96 LYS cc_start: 0.5244 (ttmt) cc_final: 0.4754 (tttm) REVERT: E 46 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7615 (mt-10) REVERT: E 60 LYS cc_start: 0.8358 (mttt) cc_final: 0.7789 (mtpt) REVERT: E 96 LYS cc_start: 0.5171 (ttmt) cc_final: 0.4500 (tttp) REVERT: F 45 LYS cc_start: 0.7531 (OUTLIER) cc_final: 0.6961 (ptpt) REVERT: F 46 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7585 (mt-10) REVERT: F 60 LYS cc_start: 0.8322 (mttt) cc_final: 0.7769 (mtpt) REVERT: F 94 PHE cc_start: 0.7880 (p90) cc_final: 0.7548 (p90) REVERT: F 96 LYS cc_start: 0.5121 (ttmt) cc_final: 0.4510 (tttp) REVERT: G 96 LYS cc_start: 0.4496 (ttmt) cc_final: 0.4033 (tttm) REVERT: H 60 LYS cc_start: 0.7978 (mttt) cc_final: 0.7511 (mttp) REVERT: H 96 LYS cc_start: 0.4949 (ttmt) cc_final: 0.4462 (tttm) REVERT: I 57 GLU cc_start: 0.8512 (pt0) cc_final: 0.8287 (pt0) REVERT: I 60 LYS cc_start: 0.8256 (mttt) cc_final: 0.7490 (tttm) REVERT: I 94 PHE cc_start: 0.7919 (p90) cc_final: 0.5118 (m-80) REVERT: I 96 LYS cc_start: 0.5057 (ttmt) cc_final: 0.4491 (tttp) REVERT: J 60 LYS cc_start: 0.8086 (mttt) cc_final: 0.7339 (tttm) REVERT: J 94 PHE cc_start: 0.7836 (p90) cc_final: 0.5356 (t80) REVERT: J 96 LYS cc_start: 0.4776 (ttmt) cc_final: 0.4350 (tttm) outliers start: 50 outliers final: 43 residues processed: 97 average time/residue: 0.4454 time to fit residues: 44.9199 Evaluate side-chains 110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 65 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 12 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.206599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.176987 restraints weight = 4345.513| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 2.59 r_work: 0.4373 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4263 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4080 Z= 0.204 Angle : 0.725 8.220 5510 Z= 0.429 Chirality : 0.059 0.264 720 Planarity : 0.003 0.018 680 Dihedral : 5.353 15.914 590 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 11.95 % Allowed : 14.63 % Favored : 73.41 % 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: -3.38 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 39 PHE 0.010 0.002 PHE D 94 HIS 0.015 0.008 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 4080) covalent geometry : angle 0.72484 ( 5510) hydrogen bonds : bond 0.02659 ( 95) hydrogen bonds : angle 5.97868 ( 279) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 68 time to evaluate : 0.120 Fit side-chains REVERT: A 60 LYS cc_start: 0.8636 (mttt) cc_final: 0.8185 (mttp) REVERT: A 96 LYS cc_start: 0.6433 (ttmt) cc_final: 0.5804 (tttp) REVERT: B 60 LYS cc_start: 0.8398 (mttt) cc_final: 0.7958 (mtpt) REVERT: B 96 LYS cc_start: 0.6469 (ttmt) cc_final: 0.5723 (tttm) REVERT: C 60 LYS cc_start: 0.8251 (mttt) cc_final: 0.7945 (mttp) REVERT: C 96 LYS cc_start: 0.5603 (ttmt) cc_final: 0.5258 (tttm) REVERT: D 60 LYS cc_start: 0.8316 (mttt) cc_final: 0.7889 (mttp) REVERT: D 94 PHE cc_start: 0.7716 (p90) cc_final: 0.7342 (p90) REVERT: D 96 LYS cc_start: 0.5234 (ttmt) cc_final: 0.4745 (tttm) REVERT: E 46 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7552 (mt-10) REVERT: E 60 LYS cc_start: 0.8345 (mttt) cc_final: 0.7766 (mtpt) REVERT: E 96 LYS cc_start: 0.5133 (ttmt) cc_final: 0.4465 (tttp) REVERT: F 45 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.6947 (ptpt) REVERT: F 46 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7570 (mt-10) REVERT: F 60 LYS cc_start: 0.8296 (mttt) cc_final: 0.7735 (mtpt) REVERT: F 94 PHE cc_start: 0.7875 (p90) cc_final: 0.7535 (p90) REVERT: F 96 LYS cc_start: 0.5115 (ttmt) cc_final: 0.4541 (tttp) REVERT: G 96 LYS cc_start: 0.4451 (ttmt) cc_final: 0.3993 (tttm) REVERT: H 60 LYS cc_start: 0.7952 (mttt) cc_final: 0.7472 (mttp) REVERT: H 96 LYS cc_start: 0.4934 (ttmt) cc_final: 0.4445 (tttm) REVERT: I 60 LYS cc_start: 0.8238 (mttt) cc_final: 0.7451 (tttm) REVERT: I 94 PHE cc_start: 0.7915 (p90) cc_final: 0.5099 (m-80) REVERT: I 96 LYS cc_start: 0.4991 (ttmt) cc_final: 0.4402 (tttp) REVERT: J 60 LYS cc_start: 0.8073 (mttt) cc_final: 0.7293 (tttm) REVERT: J 94 PHE cc_start: 0.7825 (p90) cc_final: 0.5354 (t80) REVERT: J 96 LYS cc_start: 0.4746 (ttmt) cc_final: 0.4325 (tttm) outliers start: 49 outliers final: 44 residues processed: 97 average time/residue: 0.4141 time to fit residues: 41.7658 Evaluate side-chains 111 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 65 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 5 optimal weight: 30.0000 chunk 38 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.219276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.189940 restraints weight = 4382.909| |-----------------------------------------------------------------------------| r_work (start): 0.4597 rms_B_bonded: 2.59 r_work: 0.4505 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4388 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 4080 Z= 0.116 Angle : 0.589 6.497 5510 Z= 0.351 Chirality : 0.054 0.217 720 Planarity : 0.003 0.017 680 Dihedral : 4.705 17.981 590 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 10.73 % Allowed : 15.85 % Favored : 73.41 % 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: -3.13 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.010 0.002 PHE D 94 HIS 0.014 0.006 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 4080) covalent geometry : angle 0.58947 ( 5510) hydrogen bonds : bond 0.02091 ( 95) hydrogen bonds : angle 5.52598 ( 279) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.129 Fit side-chains revert: symmetry clash REVERT: A 60 LYS cc_start: 0.8570 (mttt) cc_final: 0.8142 (mttp) REVERT: A 96 LYS cc_start: 0.6484 (ttmt) cc_final: 0.5831 (tttp) REVERT: B 60 LYS cc_start: 0.8390 (mttt) cc_final: 0.7915 (mtpt) REVERT: B 96 LYS cc_start: 0.6487 (ttmt) cc_final: 0.5847 (tttm) REVERT: C 60 LYS cc_start: 0.8275 (mttt) cc_final: 0.7996 (mttm) REVERT: C 96 LYS cc_start: 0.5819 (ttmt) cc_final: 0.5368 (tttm) REVERT: D 60 LYS cc_start: 0.8326 (mttt) cc_final: 0.7919 (mttp) REVERT: D 94 PHE cc_start: 0.7599 (p90) cc_final: 0.7278 (p90) REVERT: D 96 LYS cc_start: 0.5449 (ttmt) cc_final: 0.4872 (tttm) REVERT: E 46 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 94 PHE cc_start: 0.7745 (p90) cc_final: 0.7422 (p90) REVERT: E 96 LYS cc_start: 0.5236 (ttmt) cc_final: 0.4518 (tttp) REVERT: F 45 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.6855 (ptpt) REVERT: F 60 LYS cc_start: 0.8308 (mttt) cc_final: 0.7952 (mttm) REVERT: F 94 PHE cc_start: 0.7879 (p90) cc_final: 0.7615 (p90) REVERT: F 96 LYS cc_start: 0.5229 (ttmt) cc_final: 0.4619 (tttp) REVERT: G 45 LYS cc_start: 0.6892 (ptmt) cc_final: 0.6684 (ptpt) REVERT: G 96 LYS cc_start: 0.4519 (ttmt) cc_final: 0.4068 (tttm) REVERT: H 60 LYS cc_start: 0.7863 (mttt) cc_final: 0.7446 (mttp) REVERT: H 96 LYS cc_start: 0.4919 (ttmt) cc_final: 0.4463 (tttp) REVERT: I 60 LYS cc_start: 0.8186 (mttt) cc_final: 0.7494 (tttm) REVERT: I 94 PHE cc_start: 0.7818 (p90) cc_final: 0.5050 (m-80) REVERT: I 96 LYS cc_start: 0.5290 (ttmt) cc_final: 0.4682 (tttp) REVERT: J 60 LYS cc_start: 0.8037 (mttt) cc_final: 0.7367 (tttp) REVERT: J 94 PHE cc_start: 0.7878 (p90) cc_final: 0.5351 (t80) REVERT: J 96 LYS cc_start: 0.5101 (ttmt) cc_final: 0.4607 (tttm) outliers start: 44 outliers final: 36 residues processed: 103 average time/residue: 0.3864 time to fit residues: 41.4197 Evaluate side-chains 110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 73 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 33 optimal weight: 0.0020 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.216266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.186601 restraints weight = 4319.367| |-----------------------------------------------------------------------------| r_work (start): 0.4570 rms_B_bonded: 2.59 r_work: 0.4474 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4359 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4080 Z= 0.140 Angle : 0.637 6.975 5510 Z= 0.378 Chirality : 0.056 0.236 720 Planarity : 0.003 0.018 680 Dihedral : 4.905 17.222 590 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 9.27 % Allowed : 16.34 % Favored : 74.39 % 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: -3.07 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.009 0.002 PHE D 94 HIS 0.015 0.007 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4080) covalent geometry : angle 0.63651 ( 5510) hydrogen bonds : bond 0.02238 ( 95) hydrogen bonds : angle 5.62594 ( 279) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1140 Ramachandran restraints generated. 570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 71 time to evaluate : 0.144 Fit side-chains REVERT: A 60 LYS cc_start: 0.8659 (mttt) cc_final: 0.8224 (mttp) REVERT: A 96 LYS cc_start: 0.6444 (ttmt) cc_final: 0.5835 (tttp) REVERT: B 60 LYS cc_start: 0.8332 (mttt) cc_final: 0.7871 (mtpt) REVERT: B 96 LYS cc_start: 0.6539 (ttmt) cc_final: 0.5886 (tttm) REVERT: C 60 LYS cc_start: 0.8237 (mttt) cc_final: 0.7948 (mttm) REVERT: C 96 LYS cc_start: 0.6012 (ttmt) cc_final: 0.5528 (tttm) REVERT: D 60 LYS cc_start: 0.8334 (mttt) cc_final: 0.7940 (mttp) REVERT: D 94 PHE cc_start: 0.7604 (p90) cc_final: 0.7292 (p90) REVERT: D 96 LYS cc_start: 0.5551 (ttmt) cc_final: 0.4959 (tttp) REVERT: E 46 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7557 (mt-10) REVERT: E 57 GLU cc_start: 0.8411 (pt0) cc_final: 0.8125 (pt0) REVERT: E 94 PHE cc_start: 0.7801 (p90) cc_final: 0.7491 (p90) REVERT: E 96 LYS cc_start: 0.5284 (ttmt) cc_final: 0.4554 (tttp) REVERT: F 45 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6885 (ptpt) REVERT: F 46 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: F 60 LYS cc_start: 0.8325 (mttt) cc_final: 0.7962 (mttm) REVERT: F 94 PHE cc_start: 0.7906 (p90) cc_final: 0.7635 (p90) REVERT: F 96 LYS cc_start: 0.5280 (ttmt) cc_final: 0.4701 (tttp) REVERT: G 96 LYS cc_start: 0.4508 (ttmt) cc_final: 0.4052 (tttm) REVERT: H 60 LYS cc_start: 0.7858 (mttt) cc_final: 0.7435 (mttp) REVERT: H 96 LYS cc_start: 0.4996 (ttmt) cc_final: 0.4494 (tttp) REVERT: I 60 LYS cc_start: 0.8186 (mttt) cc_final: 0.7500 (tttp) REVERT: I 94 PHE cc_start: 0.7845 (p90) cc_final: 0.5032 (m-80) REVERT: I 96 LYS cc_start: 0.5250 (ttmt) cc_final: 0.4639 (tttp) REVERT: J 60 LYS cc_start: 0.8137 (mttt) cc_final: 0.7363 (tttp) REVERT: J 94 PHE cc_start: 0.7871 (p90) cc_final: 0.5361 (t80) REVERT: J 96 LYS cc_start: 0.5103 (ttmt) cc_final: 0.4584 (tttm) outliers start: 38 outliers final: 36 residues processed: 92 average time/residue: 0.3985 time to fit residues: 38.1746 Evaluate side-chains 106 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 0.5980 chunk 14 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4882 r_free = 0.4882 target = 0.224203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.194735 restraints weight = 4275.492| |-----------------------------------------------------------------------------| r_work (start): 0.4662 rms_B_bonded: 2.63 r_work: 0.4563 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.4450 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4080 Z= 0.106 Angle : 0.570 5.896 5510 Z= 0.339 Chirality : 0.054 0.206 720 Planarity : 0.003 0.018 680 Dihedral : 4.543 17.897 590 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 9.02 % Allowed : 16.83 % Favored : 74.15 % 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: -2.92 (0.29), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.010 0.002 PHE D 94 HIS 0.014 0.005 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 4080) covalent geometry : angle 0.56958 ( 5510) hydrogen bonds : bond 0.01864 ( 95) hydrogen bonds : angle 5.33685 ( 279) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1474.19 seconds wall clock time: 25 minutes 51.43 seconds (1551.43 seconds total)