Starting phenix.real_space_refine on Sat Apr 4 20:41:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rbb_53890/04_2026/9rbb_53890.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rbb_53890/04_2026/9rbb_53890.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rbb_53890/04_2026/9rbb_53890.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rbb_53890/04_2026/9rbb_53890.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rbb_53890/04_2026/9rbb_53890.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rbb_53890/04_2026/9rbb_53890.map" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 1940 2.51 5 N 560 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 316 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.31, per 1000 atoms: 0.10 Number of scatterers: 3160 At special positions: 0 Unit cell: (87.74, 82.82, 40.18, 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 660 8.00 N 560 7.00 C 1940 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: 0.24 Conformation dependent library (CDL) restraints added in 135.2 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 55.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 55 removed outlier: 6.447A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY A 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N THR C 54 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS C 45 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL E 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLY C 47 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N HIS E 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N VAL C 49 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.026A pdb=" N VAL E 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLY C 51 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR E 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LYS E 45 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL G 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLY E 47 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 10.124A pdb=" N HIS G 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N VAL E 49 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N VAL G 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY E 51 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR G 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LYS G 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL I 48 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY G 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N HIS I 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N VAL G 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N VAL I 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLY G 51 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR I 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 66 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 72 removed outlier: 6.648A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N THR E 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL C 71 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR G 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL E 71 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N THR I 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL G 71 " --> pdb=" O THR I 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 81 removed outlier: 5.897A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LYS C 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N GLN A 79 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ALA E 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LYS E 80 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN C 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N LYS G 80 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN E 79 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR G 75 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ALA I 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL G 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N LYS I 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLN G 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 55 removed outlier: 6.805A pdb=" N VAL D 48 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL B 49 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS D 50 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N HIS F 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N THR F 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS F 45 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL H 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLY F 47 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N HIS H 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL F 49 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 9.033A pdb=" N VAL H 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY F 51 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR H 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LYS H 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL J 48 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY H 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N HIS J 50 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N VAL H 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N VAL J 52 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY H 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR J 54 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 66 Processing sheet with id=AA8, first strand: chain 'B' and resid 69 through 72 removed outlier: 6.677A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N THR D 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N THR F 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N VAL D 71 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N THR H 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL F 71 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA H 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR J 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL H 71 " --> pdb=" O THR J 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 75 through 81 removed outlier: 5.908A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N LYS D 80 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN B 79 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N ALA F 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LYS F 80 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLN D 79 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N LYS H 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N GLN F 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR H 75 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ALA J 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL H 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N LYS J 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN H 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 87 through 88 62 hydrogen bonds defined for protein. 186 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: 0.43 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.27: 580 1.27 - 1.35: 504 1.35 - 1.44: 46 1.44 - 1.52: 854 1.52 - 1.60: 1176 Bond restraints: 3160 Sorted by residual: bond pdb=" C VAL D 52 " pdb=" O VAL D 52 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.10e-02 8.26e+03 1.94e+01 bond pdb=" C VAL H 52 " pdb=" O VAL H 52 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" C VAL E 52 " pdb=" O VAL E 52 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.10e-02 8.26e+03 1.93e+01 bond pdb=" C VAL I 52 " pdb=" O VAL I 52 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.10e-02 8.26e+03 1.92e+01 bond pdb=" C VAL C 52 " pdb=" O VAL C 52 " ideal model delta sigma weight residual 1.237 1.189 0.048 1.10e-02 8.26e+03 1.92e+01 ... (remaining 3155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 3784 3.50 - 7.00: 451 7.00 - 10.50: 45 10.50 - 14.00: 0 14.00 - 17.50: 10 Bond angle restraints: 4290 Sorted by residual: angle pdb=" N GLU A 57 " pdb=" CA GLU A 57 " pdb=" C GLU A 57 " ideal model delta sigma weight residual 111.28 128.78 -17.50 1.09e+00 8.42e-01 2.58e+02 angle pdb=" N GLU C 57 " pdb=" CA GLU C 57 " pdb=" C GLU C 57 " ideal model delta sigma weight residual 111.28 128.77 -17.49 1.09e+00 8.42e-01 2.58e+02 angle pdb=" N GLU E 57 " pdb=" CA GLU E 57 " pdb=" C GLU E 57 " ideal model delta sigma weight residual 111.28 128.77 -17.49 1.09e+00 8.42e-01 2.57e+02 angle pdb=" N GLU I 57 " pdb=" CA GLU I 57 " pdb=" C GLU I 57 " ideal model delta sigma weight residual 111.28 128.77 -17.49 1.09e+00 8.42e-01 2.57e+02 angle pdb=" N GLU F 57 " pdb=" CA GLU F 57 " pdb=" C GLU F 57 " ideal model delta sigma weight residual 111.28 128.76 -17.48 1.09e+00 8.42e-01 2.57e+02 ... (remaining 4285 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1689 16.43 - 32.86: 101 32.86 - 49.29: 40 49.29 - 65.72: 10 65.72 - 82.15: 10 Dihedral angle restraints: 1850 sinusoidal: 590 harmonic: 1260 Sorted by residual: dihedral pdb=" C LYS D 58 " pdb=" N LYS D 58 " pdb=" CA LYS D 58 " pdb=" CB LYS D 58 " ideal model delta harmonic sigma weight residual -122.60 -131.70 9.10 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C LYS F 58 " pdb=" N LYS F 58 " pdb=" CA LYS F 58 " pdb=" CB LYS F 58 " ideal model delta harmonic sigma weight residual -122.60 -131.67 9.07 0 2.50e+00 1.60e-01 1.32e+01 dihedral pdb=" C LYS B 58 " pdb=" N LYS B 58 " pdb=" CA LYS B 58 " pdb=" CB LYS B 58 " ideal model delta harmonic sigma weight residual -122.60 -131.66 9.06 0 2.50e+00 1.60e-01 1.31e+01 ... (remaining 1847 not shown) Histogram of chiral volume deviations from ideal: 0.005 - 0.060: 251 0.060 - 0.114: 178 0.114 - 0.169: 102 0.169 - 0.223: 29 0.223 - 0.278: 30 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA LYS D 58 " pdb=" N LYS D 58 " pdb=" C LYS D 58 " pdb=" CB LYS D 58 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS F 58 " pdb=" N LYS F 58 " pdb=" C LYS F 58 " pdb=" CB LYS F 58 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA LYS H 58 " pdb=" N LYS H 58 " pdb=" C LYS H 58 " pdb=" CB LYS H 58 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 587 not shown) Planarity restraints: 540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 53 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" C ALA E 53 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA E 53 " -0.016 2.00e-02 2.50e+03 pdb=" N THR E 54 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 53 " -0.012 2.00e-02 2.50e+03 2.45e-02 5.99e+00 pdb=" C ALA G 53 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA G 53 " -0.016 2.00e-02 2.50e+03 pdb=" N THR G 54 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA J 53 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.98e+00 pdb=" C ALA J 53 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA J 53 " 0.016 2.00e-02 2.50e+03 pdb=" N THR J 54 " 0.014 2.00e-02 2.50e+03 ... (remaining 537 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1705 3.00 - 3.47: 2955 3.47 - 3.95: 4802 3.95 - 4.42: 5980 4.42 - 4.90: 11352 Nonbonded interactions: 26794 Sorted by model distance: nonbonded pdb=" N GLY J 67 " pdb=" O GLY J 67 " model vdw 2.520 2.496 nonbonded pdb=" N GLY I 67 " pdb=" O GLY I 67 " model vdw 2.521 2.496 nonbonded pdb=" N GLY H 67 " pdb=" O GLY H 67 " model vdw 2.521 2.496 nonbonded pdb=" N GLY D 67 " pdb=" O GLY D 67 " model vdw 2.521 2.496 nonbonded pdb=" N GLY A 67 " pdb=" O GLY A 67 " model vdw 2.521 2.496 ... (remaining 26789 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: 1.670 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.650 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.022 0.081 3160 Z= 1.402 Angle : 2.390 17.496 4290 Z= 1.778 Chirality : 0.106 0.278 590 Planarity : 0.008 0.025 540 Dihedral : 15.974 82.145 1050 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.12 % Allowed : 9.38 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.38), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.01 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.02216 ( 3160) covalent geometry : angle 2.38956 ( 4290) hydrogen bonds : bond 0.12574 ( 62) hydrogen bonds : angle 6.77714 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.074 Fit side-chains REVERT: D 60 LYS cc_start: 0.8108 (tttm) cc_final: 0.7845 (tttt) outliers start: 10 outliers final: 0 residues processed: 149 average time/residue: 0.0526 time to fit residues: 9.5369 Evaluate side-chains 93 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4228 r_free = 0.4228 target = 0.161044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.146537 restraints weight = 3869.172| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 2.61 r_work: 0.4002 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3891 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3160 Z= 0.131 Angle : 0.511 3.234 4290 Z= 0.311 Chirality : 0.051 0.135 590 Planarity : 0.003 0.016 540 Dihedral : 5.970 14.990 460 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 9.06 % Allowed : 12.50 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.38), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.10 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.003 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 3160) covalent geometry : angle 0.51126 ( 4290) hydrogen bonds : bond 0.01879 ( 62) hydrogen bonds : angle 5.03701 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 59 time to evaluate : 0.071 Fit side-chains REVERT: A 62 GLN cc_start: 0.8342 (tt0) cc_final: 0.7878 (tt0) REVERT: I 46 GLU cc_start: 0.5817 (tt0) cc_final: 0.5559 (tt0) REVERT: I 54 THR cc_start: 0.8360 (m) cc_final: 0.8138 (p) outliers start: 29 outliers final: 26 residues processed: 83 average time/residue: 0.0551 time to fit residues: 5.7329 Evaluate side-chains 81 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 0.0020 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.153587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.139380 restraints weight = 3916.712| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.61 r_work: 0.3907 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 3160 Z= 0.164 Angle : 0.470 2.610 4290 Z= 0.290 Chirality : 0.053 0.125 590 Planarity : 0.002 0.014 540 Dihedral : 5.723 13.856 460 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 11.56 % Allowed : 10.94 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.37), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.32 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 3160) covalent geometry : angle 0.47042 ( 4290) hydrogen bonds : bond 0.01651 ( 62) hydrogen bonds : angle 5.21138 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.068 Fit side-chains REVERT: A 62 GLN cc_start: 0.8395 (tt0) cc_final: 0.7998 (tt0) outliers start: 37 outliers final: 34 residues processed: 84 average time/residue: 0.0429 time to fit residues: 4.7060 Evaluate side-chains 89 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 55 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.148955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.135032 restraints weight = 3929.151| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.56 r_work: 0.3848 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 3160 Z= 0.278 Angle : 0.521 2.800 4290 Z= 0.322 Chirality : 0.057 0.155 590 Planarity : 0.003 0.012 540 Dihedral : 6.065 14.450 460 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 13.12 % Allowed : 10.31 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.36), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.59 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00635 ( 3160) covalent geometry : angle 0.52110 ( 4290) hydrogen bonds : bond 0.01775 ( 62) hydrogen bonds : angle 5.32838 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 60 time to evaluate : 0.109 Fit side-chains REVERT: A 62 GLN cc_start: 0.8441 (tt0) cc_final: 0.8006 (tt0) outliers start: 42 outliers final: 42 residues processed: 89 average time/residue: 0.0443 time to fit residues: 5.0652 Evaluate side-chains 101 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 59 time to evaluate : 0.125 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 54 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 39 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- 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 = 0.4170 r_free = 0.4170 target = 0.155391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.141581 restraints weight = 3898.924| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 2.57 r_work: 0.3951 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3840 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3160 Z= 0.102 Angle : 0.405 2.387 4290 Z= 0.251 Chirality : 0.051 0.120 590 Planarity : 0.002 0.011 540 Dihedral : 5.325 13.313 460 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 8.12 % Allowed : 15.00 % Favored : 76.88 % 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: -0.76 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 3160) covalent geometry : angle 0.40476 ( 4290) hydrogen bonds : bond 0.01471 ( 62) hydrogen bonds : angle 4.68596 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.082 Fit side-chains REVERT: A 62 GLN cc_start: 0.8359 (tt0) cc_final: 0.7939 (tt0) outliers start: 26 outliers final: 25 residues processed: 75 average time/residue: 0.0437 time to fit residues: 4.2628 Evaluate side-chains 79 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 9.9990 chunk 8 optimal weight: 0.2980 chunk 37 optimal weight: 0.0970 chunk 4 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 = 0.4206 r_free = 0.4206 target = 0.159233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.145553 restraints weight = 3914.592| |-----------------------------------------------------------------------------| r_work (start): 0.4058 rms_B_bonded: 2.61 r_work: 0.3964 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3851 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 3160 Z= 0.093 Angle : 0.395 2.354 4290 Z= 0.245 Chirality : 0.051 0.117 590 Planarity : 0.002 0.011 540 Dihedral : 5.093 13.398 460 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 10.00 % Allowed : 12.81 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.35), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.63 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 3160) covalent geometry : angle 0.39521 ( 4290) hydrogen bonds : bond 0.01307 ( 62) hydrogen bonds : angle 4.39991 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.107 Fit side-chains REVERT: A 62 GLN cc_start: 0.8347 (tt0) cc_final: 0.7953 (tt0) outliers start: 32 outliers final: 31 residues processed: 80 average time/residue: 0.0413 time to fit residues: 4.3829 Evaluate side-chains 85 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.150318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.135754 restraints weight = 4021.479| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 2.63 r_work: 0.3877 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3160 Z= 0.156 Angle : 0.428 2.326 4290 Z= 0.264 Chirality : 0.052 0.131 590 Planarity : 0.002 0.011 540 Dihedral : 5.401 12.825 460 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 10.62 % Allowed : 13.12 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.79 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3160) covalent geometry : angle 0.42750 ( 4290) hydrogen bonds : bond 0.01325 ( 62) hydrogen bonds : angle 4.42134 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 54 time to evaluate : 0.083 Fit side-chains REVERT: A 62 GLN cc_start: 0.8409 (tt0) cc_final: 0.7981 (tt0) outliers start: 34 outliers final: 32 residues processed: 82 average time/residue: 0.0398 time to fit residues: 4.2971 Evaluate side-chains 86 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 36 optimal weight: 0.0070 chunk 8 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.150071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.135453 restraints weight = 4021.043| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.63 r_work: 0.3870 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3160 Z= 0.156 Angle : 0.428 2.302 4290 Z= 0.265 Chirality : 0.052 0.129 590 Planarity : 0.002 0.011 540 Dihedral : 5.396 12.776 460 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 10.00 % Allowed : 13.12 % Favored : 76.88 % 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: -1.14 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.86 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 3160) covalent geometry : angle 0.42753 ( 4290) hydrogen bonds : bond 0.01369 ( 62) hydrogen bonds : angle 4.39472 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.125 Fit side-chains REVERT: A 62 GLN cc_start: 0.8397 (tt0) cc_final: 0.7989 (tt0) outliers start: 32 outliers final: 32 residues processed: 81 average time/residue: 0.0425 time to fit residues: 4.5238 Evaluate side-chains 87 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.4120 r_free = 0.4120 target = 0.150662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.136120 restraints weight = 4003.161| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 2.63 r_work: 0.3889 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3773 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3160 Z= 0.142 Angle : 0.420 2.299 4290 Z= 0.260 Chirality : 0.052 0.126 590 Planarity : 0.002 0.011 540 Dihedral : 5.332 12.971 460 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 10.00 % Allowed : 13.44 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3160) covalent geometry : angle 0.41959 ( 4290) hydrogen bonds : bond 0.01359 ( 62) hydrogen bonds : angle 4.36990 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.113 Fit side-chains REVERT: A 62 GLN cc_start: 0.8427 (tt0) cc_final: 0.8033 (tt0) outliers start: 32 outliers final: 31 residues processed: 80 average time/residue: 0.0453 time to fit residues: 4.7547 Evaluate side-chains 85 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.150551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136897 restraints weight = 4109.287| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.62 r_work: 0.3872 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3160 Z= 0.125 Angle : 0.411 2.297 4290 Z= 0.254 Chirality : 0.052 0.121 590 Planarity : 0.002 0.011 540 Dihedral : 5.247 13.034 460 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 9.38 % Allowed : 13.75 % Favored : 76.88 % 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: -1.18 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.89 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3160) covalent geometry : angle 0.41091 ( 4290) hydrogen bonds : bond 0.01362 ( 62) hydrogen bonds : angle 4.32566 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.095 Fit side-chains REVERT: A 62 GLN cc_start: 0.8395 (tt0) cc_final: 0.7965 (tt0) outliers start: 30 outliers final: 30 residues processed: 77 average time/residue: 0.0432 time to fit residues: 4.3818 Evaluate side-chains 83 residues out of total 320 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 87 SER Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- 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 = 0.4086 r_free = 0.4086 target = 0.150522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.136750 restraints weight = 4148.119| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.65 r_work: 0.3873 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3761 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3160 Z= 0.125 Angle : 0.409 2.299 4290 Z= 0.253 Chirality : 0.052 0.121 590 Planarity : 0.002 0.011 540 Dihedral : 5.221 13.018 460 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 9.38 % Allowed : 13.75 % Favored : 76.88 % 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: -1.20 (0.34), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 3160) covalent geometry : angle 0.40907 ( 4290) hydrogen bonds : bond 0.01330 ( 62) hydrogen bonds : angle 4.31327 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 979.77 seconds wall clock time: 17 minutes 45.77 seconds (1065.77 seconds total)