Starting phenix.real_space_refine on Wed Mar 5 23:07:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6osl_20185/03_2025/6osl_20185.cif Found real_map, /net/cci-nas-00/data/ceres_data/6osl_20185/03_2025/6osl_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_2025/6osl_20185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2025/6osl_20185.map" model { file = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2025/6osl_20185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6osl_20185/03_2025/6osl_20185.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.52, per 1000 atoms: 0.37 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: 0.89 Conformation dependent library (CDL) restraints added in 506.3 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: 0.93 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: 1.03 Time building geometry restraints manager: 1.07 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 13.200 Find NCS groups from input model: 0.100 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:14.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- 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= 0.699 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.016 0.010 HIS B 50 PHE 0.003 0.001 PHE B 94 TYR 0.006 0.002 TYR H 39 *********************** 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 : 0.448 Fit side-chains REVERT: A 57 GLU cc_start: 0.8300 (pt0) cc_final: 0.8062 (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: 0.7280 (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: 0.5451 (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: 0.4338 (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: 0.7306 (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: 1.1477 time to fit residues: 113.8176 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 : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 = 0.206425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.177670 restraints weight = 4340.812| |-----------------------------------------------------------------------------| r_work (start): 0.4434 rms_B_bonded: 2.60 r_work: 0.4329 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 4080 Z= 0.370 Angle : 0.819 8.761 5510 Z= 0.485 Chirality : 0.063 0.273 720 Planarity : 0.004 0.019 680 Dihedral : 5.780 18.111 590 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 7.32 % Allowed : 18.54 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.01 (0.24), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.18), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.009 HIS C 50 PHE 0.006 0.001 PHE F 94 TYR 0.004 0.001 TYR B 39 *********************** 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 108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 78 time to evaluate : 0.451 Fit side-chains REVERT: A 57 GLU cc_start: 0.8526 (pt0) cc_final: 0.8240 (pt0) REVERT: A 60 LYS cc_start: 0.8701 (mttt) cc_final: 0.8245 (mttp) REVERT: A 96 LYS cc_start: 0.5883 (ttmt) cc_final: 0.5305 (tttp) REVERT: B 57 GLU cc_start: 0.8689 (pt0) cc_final: 0.8450 (pt0) REVERT: B 60 LYS cc_start: 0.8466 (mttt) cc_final: 0.8003 (mtpt) REVERT: B 96 LYS cc_start: 0.6290 (ttmt) cc_final: 0.5582 (tttm) REVERT: C 45 LYS cc_start: 0.6924 (pttt) cc_final: 0.6402 (ptpt) REVERT: C 60 LYS cc_start: 0.8361 (mttt) cc_final: 0.8048 (mttm) REVERT: C 94 PHE cc_start: 0.7981 (p90) cc_final: 0.7749 (p90) REVERT: C 96 LYS cc_start: 0.5481 (ttmt) cc_final: 0.4822 (tttm) REVERT: D 45 LYS cc_start: 0.6994 (pttt) cc_final: 0.6651 (ptpt) REVERT: D 60 LYS cc_start: 0.8410 (mttt) cc_final: 0.8077 (mttp) REVERT: D 94 PHE cc_start: 0.7801 (p90) cc_final: 0.7358 (p90) REVERT: D 96 LYS cc_start: 0.5290 (ttmt) cc_final: 0.4792 (tttm) REVERT: E 57 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: E 60 LYS cc_start: 0.8505 (mttt) cc_final: 0.7892 (mtpt) REVERT: E 94 PHE cc_start: 0.7928 (p90) cc_final: 0.7556 (p90) REVERT: E 96 LYS cc_start: 0.4880 (ttmt) cc_final: 0.4201 (tttp) REVERT: F 60 LYS cc_start: 0.8303 (mttt) cc_final: 0.7746 (mtpt) REVERT: F 94 PHE cc_start: 0.7815 (p90) cc_final: 0.7316 (p90) REVERT: F 96 LYS cc_start: 0.5329 (ttmt) cc_final: 0.4715 (tttp) REVERT: G 96 LYS cc_start: 0.4220 (ttmt) cc_final: 0.3832 (tttm) REVERT: H 60 LYS cc_start: 0.8038 (mttt) cc_final: 0.7526 (mttp) REVERT: H 96 LYS cc_start: 0.4801 (ttmt) cc_final: 0.4359 (tttp) REVERT: I 60 LYS cc_start: 0.8287 (mttt) cc_final: 0.7473 (tttm) REVERT: I 94 PHE cc_start: 0.7869 (p90) cc_final: 0.5165 (m-80) REVERT: I 96 LYS cc_start: 0.5077 (ttmt) cc_final: 0.4556 (tttp) REVERT: J 60 LYS cc_start: 0.8049 (mttt) cc_final: 0.7290 (tttm) REVERT: J 94 PHE cc_start: 0.7968 (p90) cc_final: 0.5397 (t80) REVERT: J 96 LYS cc_start: 0.4821 (ttmt) cc_final: 0.4397 (tttm) outliers start: 30 outliers final: 18 residues processed: 87 average time/residue: 1.3416 time to fit residues: 120.2493 Evaluate side-chains 90 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 54 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D 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 72 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 58 LYS Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- 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 = 0.4745 r_free = 0.4745 target = 0.212688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.183408 restraints weight = 4325.164| |-----------------------------------------------------------------------------| r_work (start): 0.4518 rms_B_bonded: 2.60 r_work: 0.4415 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.4304 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4080 Z= 0.210 Angle : 0.655 7.256 5510 Z= 0.391 Chirality : 0.057 0.230 720 Planarity : 0.003 0.016 680 Dihedral : 5.010 14.311 590 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 10.49 % Allowed : 16.34 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.008 HIS H 50 PHE 0.018 0.002 PHE A 94 TYR 0.003 0.001 TYR C 39 *********************** 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 129 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 86 time to evaluate : 0.442 Fit side-chains REVERT: A 60 LYS cc_start: 0.8703 (mttt) cc_final: 0.8252 (mttp) REVERT: A 96 LYS cc_start: 0.6096 (ttmt) cc_final: 0.5515 (tttp) REVERT: B 45 LYS cc_start: 0.6971 (pttt) cc_final: 0.6654 (ptpt) REVERT: B 57 GLU cc_start: 0.8570 (pt0) cc_final: 0.8345 (pt0) REVERT: B 60 LYS cc_start: 0.8510 (mttt) cc_final: 0.8059 (mtpt) REVERT: B 96 LYS cc_start: 0.6526 (ttmt) cc_final: 0.5786 (tttm) REVERT: C 45 LYS cc_start: 0.6737 (pttt) cc_final: 0.6429 (ptmt) REVERT: C 60 LYS cc_start: 0.8302 (mttt) cc_final: 0.8010 (mttp) REVERT: C 96 LYS cc_start: 0.5689 (ttmt) cc_final: 0.4996 (tttm) REVERT: D 60 LYS cc_start: 0.8421 (mttt) cc_final: 0.8077 (mttp) REVERT: D 94 PHE cc_start: 0.7865 (p90) cc_final: 0.7451 (p90) REVERT: D 96 LYS cc_start: 0.5351 (ttmt) cc_final: 0.4790 (tttm) REVERT: E 60 LYS cc_start: 0.8425 (mttt) cc_final: 0.7853 (mtpt) REVERT: E 94 PHE cc_start: 0.7865 (p90) cc_final: 0.7492 (p90) REVERT: E 96 LYS cc_start: 0.5165 (ttmt) cc_final: 0.4419 (tttp) REVERT: F 45 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6843 (ptpt) REVERT: F 60 LYS cc_start: 0.8344 (mttt) cc_final: 0.7796 (mtpt) REVERT: F 94 PHE cc_start: 0.7846 (p90) cc_final: 0.7428 (p90) REVERT: F 96 LYS cc_start: 0.5487 (ttmt) cc_final: 0.4850 (tttp) REVERT: G 96 LYS cc_start: 0.4411 (ttmt) cc_final: 0.3977 (tttm) REVERT: H 60 LYS cc_start: 0.8061 (mttt) cc_final: 0.7576 (mttp) REVERT: H 96 LYS cc_start: 0.5006 (ttmt) cc_final: 0.4531 (tttp) REVERT: I 60 LYS cc_start: 0.8275 (mttt) cc_final: 0.7537 (tttm) REVERT: I 94 PHE cc_start: 0.7843 (p90) cc_final: 0.5185 (m-80) REVERT: I 96 LYS cc_start: 0.5331 (ttmt) cc_final: 0.4683 (tttp) REVERT: J 60 LYS cc_start: 0.8062 (mttt) cc_final: 0.7374 (tttm) REVERT: J 94 PHE cc_start: 0.7896 (p90) cc_final: 0.5336 (t80) REVERT: J 96 LYS cc_start: 0.4958 (ttmt) cc_final: 0.4492 (tttm) outliers start: 43 outliers final: 32 residues processed: 105 average time/residue: 0.9621 time to fit residues: 105.0360 Evaluate side-chains 103 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.410 ------------------------------------------------------------------------------- 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 54 THR 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 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 54 THR 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 54 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR 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 54 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.4853 r_free = 0.4853 target = 0.222700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.194126 restraints weight = 4230.763| |-----------------------------------------------------------------------------| r_work (start): 0.4636 rms_B_bonded: 2.62 r_work: 0.4545 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.4433 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2564 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= 0.130 Angle : 0.561 5.624 5510 Z= 0.335 Chirality : 0.054 0.193 720 Planarity : 0.003 0.016 680 Dihedral : 4.530 17.945 590 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 7.80 % Allowed : 18.78 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.29), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.005 HIS H 50 PHE 0.021 0.003 PHE C 94 TYR 0.002 0.000 TYR C 39 *********************** 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 115 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 83 time to evaluate : 0.449 Fit side-chains REVERT: A 60 LYS cc_start: 0.8567 (mttt) cc_final: 0.8142 (mttp) REVERT: A 96 LYS cc_start: 0.6520 (ttmt) cc_final: 0.5877 (tttp) REVERT: B 57 GLU cc_start: 0.8470 (pt0) cc_final: 0.8230 (pt0) REVERT: B 60 LYS cc_start: 0.8472 (mttt) cc_final: 0.8002 (mtpt) REVERT: B 96 LYS cc_start: 0.6518 (ttmt) cc_final: 0.5878 (tttm) REVERT: C 60 LYS cc_start: 0.8291 (mttt) cc_final: 0.8017 (mttm) REVERT: C 96 LYS cc_start: 0.5855 (ttmt) cc_final: 0.5272 (tttm) REVERT: D 60 LYS cc_start: 0.8368 (mttt) cc_final: 0.7963 (mttp) REVERT: D 94 PHE cc_start: 0.7889 (p90) cc_final: 0.7530 (p90) REVERT: D 96 LYS cc_start: 0.5436 (ttmt) cc_final: 0.4903 (tttm) REVERT: E 57 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8335 (pt0) REVERT: E 60 LYS cc_start: 0.8377 (mttt) cc_final: 0.7837 (mtpt) REVERT: E 94 PHE cc_start: 0.7729 (p90) cc_final: 0.7420 (p90) REVERT: E 96 LYS cc_start: 0.5227 (ttmt) cc_final: 0.4447 (tttp) REVERT: F 60 LYS cc_start: 0.8300 (mttt) cc_final: 0.7937 (mttm) REVERT: F 94 PHE cc_start: 0.7779 (p90) cc_final: 0.7510 (p90) REVERT: F 96 LYS cc_start: 0.5484 (ttmt) cc_final: 0.4820 (tttp) REVERT: G 45 LYS cc_start: 0.7029 (ptmt) cc_final: 0.6614 (ptpt) REVERT: G 96 LYS cc_start: 0.4365 (ttmt) cc_final: 0.3879 (tttm) REVERT: H 60 LYS cc_start: 0.7997 (mttt) cc_final: 0.7614 (mttp) REVERT: H 96 LYS cc_start: 0.4896 (ttmt) cc_final: 0.4422 (tttm) REVERT: I 60 LYS cc_start: 0.8211 (mttt) cc_final: 0.7486 (tttm) REVERT: I 94 PHE cc_start: 0.7780 (p90) cc_final: 0.5203 (m-80) REVERT: I 96 LYS cc_start: 0.5310 (ttmt) cc_final: 0.4690 (tttp) REVERT: J 60 LYS cc_start: 0.8105 (mttt) cc_final: 0.7368 (tttm) REVERT: J 94 PHE cc_start: 0.7818 (p90) cc_final: 0.5331 (t80) REVERT: J 96 LYS cc_start: 0.5117 (ttmt) cc_final: 0.4570 (tttm) outliers start: 32 outliers final: 22 residues processed: 100 average time/residue: 0.9654 time to fit residues: 100.3165 Evaluate side-chains 95 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 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 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 81 THR Chi-restraints excluded: chain F residue 92 THR 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 58 LYS 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 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 overall best weight: 9.3990 ------------------------------------------------------------------------------- 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 = 0.4608 r_free = 0.4608 target = 0.195437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.166231 restraints weight = 4637.092| |-----------------------------------------------------------------------------| r_work (start): 0.4342 rms_B_bonded: 2.58 r_work: 0.4241 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4133 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.063 4080 Z= 0.683 Angle : 0.985 9.882 5510 Z= 0.577 Chirality : 0.069 0.315 720 Planarity : 0.004 0.023 680 Dihedral : 6.340 17.962 590 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 11.95 % Allowed : 13.41 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.010 HIS A 50 PHE 0.019 0.002 PHE A 94 TYR 0.013 0.002 TYR A 39 *********************** 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 119 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 70 time to evaluate : 0.450 Fit side-chains REVERT: A 60 LYS cc_start: 0.8634 (mttt) cc_final: 0.8206 (mttp) REVERT: A 96 LYS cc_start: 0.6454 (ttmt) cc_final: 0.5824 (tttp) REVERT: B 57 GLU cc_start: 0.8637 (pt0) cc_final: 0.8373 (pt0) REVERT: B 60 LYS cc_start: 0.8432 (mttt) cc_final: 0.7955 (mtpt) REVERT: B 96 LYS cc_start: 0.6416 (ttmt) cc_final: 0.5710 (tttm) REVERT: C 45 LYS cc_start: 0.6951 (pttt) cc_final: 0.6497 (ptmt) REVERT: C 60 LYS cc_start: 0.8299 (mttt) cc_final: 0.7972 (mttm) REVERT: C 96 LYS cc_start: 0.5545 (ttmt) cc_final: 0.5223 (tttm) REVERT: D 45 LYS cc_start: 0.7344 (pttt) cc_final: 0.6826 (ptpt) REVERT: D 60 LYS cc_start: 0.8365 (mttt) cc_final: 0.8081 (mttp) REVERT: D 96 LYS cc_start: 0.5317 (ttmt) cc_final: 0.4848 (tttm) REVERT: E 57 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: E 60 LYS cc_start: 0.8426 (mttt) cc_final: 0.7851 (mtpt) REVERT: E 96 LYS cc_start: 0.5025 (ttmt) cc_final: 0.4478 (tttp) REVERT: F 46 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7648 (mt-10) REVERT: F 60 LYS cc_start: 0.8318 (mttt) cc_final: 0.7766 (mtpt) REVERT: F 94 PHE cc_start: 0.7958 (p90) cc_final: 0.7567 (p90) REVERT: F 96 LYS cc_start: 0.5326 (ttmt) cc_final: 0.4737 (tttp) REVERT: G 96 LYS cc_start: 0.4599 (ttmt) cc_final: 0.4162 (tttm) REVERT: H 60 LYS cc_start: 0.8129 (mttt) cc_final: 0.7630 (mttp) REVERT: H 96 LYS cc_start: 0.4845 (ttmt) cc_final: 0.4355 (tttp) REVERT: I 60 LYS cc_start: 0.8360 (mttt) cc_final: 0.7542 (tttm) REVERT: I 94 PHE cc_start: 0.8004 (p90) cc_final: 0.5028 (m-80) REVERT: I 96 LYS cc_start: 0.5320 (ttmt) cc_final: 0.4669 (tttp) REVERT: J 60 LYS cc_start: 0.8100 (mttt) cc_final: 0.7404 (tttp) REVERT: J 94 PHE cc_start: 0.7840 (p90) cc_final: 0.5284 (t80) REVERT: J 96 LYS cc_start: 0.4935 (ttmt) cc_final: 0.4363 (tmtm) outliers start: 49 outliers final: 40 residues processed: 102 average time/residue: 1.0155 time to fit residues: 107.4842 Evaluate side-chains 108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 57 GLU 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 45 LYS 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 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 54 THR 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 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 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 58 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4779 r_free = 0.4779 target = 0.214990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.185621 restraints weight = 4297.400| |-----------------------------------------------------------------------------| r_work (start): 0.4542 rms_B_bonded: 2.59 r_work: 0.4453 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4344 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.4344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2498 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= 0.176 Angle : 0.619 6.729 5510 Z= 0.368 Chirality : 0.055 0.222 720 Planarity : 0.003 0.019 680 Dihedral : 5.018 17.011 590 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 8.78 % Allowed : 18.29 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.014 0.006 HIS H 50 PHE 0.017 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 *********************** 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 118 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.456 Fit side-chains REVERT: A 60 LYS cc_start: 0.8611 (mttt) cc_final: 0.8151 (mttp) REVERT: A 96 LYS cc_start: 0.6396 (ttmt) cc_final: 0.5753 (tttp) REVERT: B 45 LYS cc_start: 0.7161 (pttt) cc_final: 0.6931 (ptpt) REVERT: B 57 GLU cc_start: 0.8489 (pt0) cc_final: 0.8232 (pt0) REVERT: B 60 LYS cc_start: 0.8388 (mttt) cc_final: 0.7883 (mtpt) REVERT: B 96 LYS cc_start: 0.6453 (ttmt) cc_final: 0.5717 (tttm) REVERT: C 60 LYS cc_start: 0.8220 (mttt) cc_final: 0.7936 (mttm) REVERT: C 96 LYS cc_start: 0.5525 (ttmt) cc_final: 0.5166 (tttm) REVERT: D 60 LYS cc_start: 0.8309 (mttt) cc_final: 0.7874 (mttp) REVERT: D 96 LYS cc_start: 0.5265 (ttmt) cc_final: 0.4664 (tttm) REVERT: E 57 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8328 (pt0) REVERT: E 60 LYS cc_start: 0.8378 (mttt) cc_final: 0.7823 (mtpt) REVERT: E 94 PHE cc_start: 0.7845 (p90) cc_final: 0.7464 (p90) REVERT: E 96 LYS cc_start: 0.5072 (ttmt) cc_final: 0.4379 (tttp) REVERT: F 46 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: F 60 LYS cc_start: 0.8261 (mttt) cc_final: 0.7711 (mtpt) REVERT: F 94 PHE cc_start: 0.7838 (p90) cc_final: 0.7617 (p90) REVERT: F 96 LYS cc_start: 0.5270 (ttmt) cc_final: 0.4636 (tttp) REVERT: G 96 LYS cc_start: 0.4451 (ttmt) cc_final: 0.4001 (tttm) REVERT: H 60 LYS cc_start: 0.7978 (mttt) cc_final: 0.7463 (mttp) REVERT: H 96 LYS cc_start: 0.4879 (ttmt) cc_final: 0.4393 (tttp) REVERT: I 57 GLU cc_start: 0.8568 (pt0) cc_final: 0.8272 (pt0) REVERT: I 60 LYS cc_start: 0.8212 (mttt) cc_final: 0.7460 (tttm) REVERT: I 94 PHE cc_start: 0.7848 (p90) cc_final: 0.5097 (m-80) REVERT: I 96 LYS cc_start: 0.4920 (ttmt) cc_final: 0.4330 (tttp) REVERT: J 60 LYS cc_start: 0.7977 (mttt) cc_final: 0.7266 (tttp) REVERT: J 94 PHE cc_start: 0.7919 (p90) cc_final: 0.5289 (t80) REVERT: J 96 LYS cc_start: 0.4820 (ttmt) cc_final: 0.4385 (tttm) outliers start: 36 outliers final: 30 residues processed: 102 average time/residue: 0.9591 time to fit residues: 101.6856 Evaluate side-chains 105 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 73 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 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 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR 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 72 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 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 47 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 5 optimal weight: 30.0000 chunk 30 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 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 = 0.4684 r_free = 0.4684 target = 0.203691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.174021 restraints weight = 4495.526| |-----------------------------------------------------------------------------| r_work (start): 0.4421 rms_B_bonded: 2.61 r_work: 0.4333 rms_B_bonded: 2.76 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: 0.7706 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 4080 Z= 0.394 Angle : 0.792 8.686 5510 Z= 0.469 Chirality : 0.061 0.287 720 Planarity : 0.004 0.019 680 Dihedral : 5.643 14.923 590 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 11.22 % Allowed : 16.34 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.008 HIS F 50 PHE 0.015 0.002 PHE C 94 TYR 0.007 0.001 TYR A 39 *********************** 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 110 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 64 time to evaluate : 0.654 Fit side-chains REVERT: A 60 LYS cc_start: 0.8596 (mttt) cc_final: 0.8082 (mttp) REVERT: A 96 LYS cc_start: 0.6397 (ttmt) cc_final: 0.5758 (tttp) REVERT: B 57 GLU cc_start: 0.8587 (pt0) cc_final: 0.8327 (pt0) REVERT: B 60 LYS cc_start: 0.8377 (mttt) cc_final: 0.7886 (mtpt) REVERT: B 96 LYS cc_start: 0.6381 (ttmt) cc_final: 0.5653 (tttm) REVERT: C 60 LYS cc_start: 0.8200 (mttt) cc_final: 0.7879 (mttp) REVERT: C 96 LYS cc_start: 0.5519 (ttmt) cc_final: 0.5184 (tttm) REVERT: D 60 LYS cc_start: 0.8293 (mttt) cc_final: 0.7909 (mttp) REVERT: D 94 PHE cc_start: 0.7775 (p90) cc_final: 0.7515 (p90) REVERT: D 96 LYS cc_start: 0.5147 (ttmt) cc_final: 0.4618 (tttm) REVERT: E 46 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7466 (mt-10) REVERT: E 57 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: E 60 LYS cc_start: 0.8345 (mttt) cc_final: 0.7717 (mtpt) REVERT: E 96 LYS cc_start: 0.4845 (ttmt) cc_final: 0.4299 (tttp) REVERT: F 46 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7673 (mt-10) REVERT: F 60 LYS cc_start: 0.8242 (mttt) cc_final: 0.7675 (mtpt) REVERT: F 94 PHE cc_start: 0.7779 (p90) cc_final: 0.7455 (p90) REVERT: F 96 LYS cc_start: 0.5175 (ttmt) cc_final: 0.4626 (tttp) REVERT: G 96 LYS cc_start: 0.4363 (ttmt) cc_final: 0.3933 (tttm) REVERT: H 60 LYS cc_start: 0.7951 (mttt) cc_final: 0.7472 (mttp) REVERT: H 96 LYS cc_start: 0.4901 (ttmt) cc_final: 0.4398 (tttp) REVERT: I 57 GLU cc_start: 0.8527 (pt0) cc_final: 0.8315 (pt0) REVERT: I 60 LYS cc_start: 0.8227 (mttt) cc_final: 0.7411 (tttm) REVERT: I 94 PHE cc_start: 0.7928 (p90) cc_final: 0.5081 (m-80) REVERT: I 96 LYS cc_start: 0.4998 (ttmt) cc_final: 0.4391 (tttp) REVERT: J 60 LYS cc_start: 0.7998 (mttt) cc_final: 0.7269 (tttm) REVERT: J 94 PHE cc_start: 0.7844 (p90) cc_final: 0.5324 (t80) REVERT: J 96 LYS cc_start: 0.4699 (ttmt) cc_final: 0.4220 (tmtm) outliers start: 46 outliers final: 40 residues processed: 91 average time/residue: 0.9988 time to fit residues: 94.5110 Evaluate side-chains 106 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 64 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 57 GLU 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 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 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 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 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 17 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4785 r_free = 0.4785 target = 0.215187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.185698 restraints weight = 4268.961| |-----------------------------------------------------------------------------| r_work (start): 0.4543 rms_B_bonded: 2.58 r_work: 0.4454 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4346 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2624 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= 0.185 Angle : 0.618 6.565 5510 Z= 0.368 Chirality : 0.055 0.231 720 Planarity : 0.003 0.017 680 Dihedral : 4.968 16.995 590 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 10.00 % Allowed : 17.32 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.007 HIS H 50 PHE 0.015 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 *********************** 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 118 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 0.416 Fit side-chains REVERT: A 60 LYS cc_start: 0.8545 (mttt) cc_final: 0.8063 (mttp) REVERT: A 96 LYS cc_start: 0.6377 (ttmt) cc_final: 0.5737 (tttp) REVERT: B 57 GLU cc_start: 0.8495 (pt0) cc_final: 0.8212 (pt0) REVERT: B 60 LYS cc_start: 0.8381 (mttt) cc_final: 0.7832 (mtpt) REVERT: B 96 LYS cc_start: 0.6575 (ttmt) cc_final: 0.5814 (tttm) REVERT: C 60 LYS cc_start: 0.8194 (mttt) cc_final: 0.7896 (mttm) REVERT: C 96 LYS cc_start: 0.5651 (ttmt) cc_final: 0.5260 (tttm) REVERT: D 60 LYS cc_start: 0.8267 (mttt) cc_final: 0.7824 (mttp) REVERT: D 96 LYS cc_start: 0.5280 (ttmt) cc_final: 0.4747 (tttm) REVERT: E 46 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7403 (mt-10) REVERT: E 57 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8311 (pt0) REVERT: E 60 LYS cc_start: 0.8346 (mttt) cc_final: 0.7791 (mtpt) REVERT: E 94 PHE cc_start: 0.7835 (p90) cc_final: 0.7463 (p90) REVERT: E 96 LYS cc_start: 0.5049 (ttmt) cc_final: 0.4357 (tttp) REVERT: F 46 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7444 (mt-10) REVERT: F 60 LYS cc_start: 0.8256 (mttt) cc_final: 0.7671 (mtpt) REVERT: F 94 PHE cc_start: 0.7831 (p90) cc_final: 0.7598 (p90) REVERT: F 96 LYS cc_start: 0.5204 (ttmt) cc_final: 0.4631 (tttp) REVERT: G 45 LYS cc_start: 0.6800 (ptmt) cc_final: 0.6508 (ptpt) REVERT: G 96 LYS cc_start: 0.4357 (ttmt) cc_final: 0.3913 (tttm) REVERT: H 60 LYS cc_start: 0.7815 (mttt) cc_final: 0.7372 (mttp) REVERT: H 96 LYS cc_start: 0.4765 (ttmt) cc_final: 0.4279 (tttp) REVERT: I 57 GLU cc_start: 0.8430 (pt0) cc_final: 0.8150 (pt0) REVERT: I 60 LYS cc_start: 0.8095 (mttt) cc_final: 0.7350 (tttm) REVERT: I 94 PHE cc_start: 0.7833 (p90) cc_final: 0.5069 (m-80) REVERT: I 96 LYS cc_start: 0.5013 (ttmt) cc_final: 0.4446 (tttp) REVERT: J 60 LYS cc_start: 0.7984 (mttt) cc_final: 0.7262 (tttm) REVERT: J 94 PHE cc_start: 0.7862 (p90) cc_final: 0.5235 (t80) REVERT: J 96 LYS cc_start: 0.4832 (ttmt) cc_final: 0.4409 (tttm) outliers start: 41 outliers final: 36 residues processed: 100 average time/residue: 0.8834 time to fit residues: 92.3014 Evaluate side-chains 111 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 73 time to evaluate : 0.464 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 49 VAL 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 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 46 GLU 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 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: 5.9990 chunk 18 optimal weight: 0.0020 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 5 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 overall best weight: 1.9394 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.217250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.187768 restraints weight = 4289.998| |-----------------------------------------------------------------------------| r_work (start): 0.4569 rms_B_bonded: 2.60 r_work: 0.4479 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4367 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4080 Z= 0.176 Angle : 0.610 6.742 5510 Z= 0.364 Chirality : 0.054 0.220 720 Planarity : 0.003 0.017 680 Dihedral : 4.759 15.523 590 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 9.27 % Allowed : 17.80 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.006 HIS H 50 PHE 0.013 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 *********************** 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 112 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 74 time to evaluate : 0.378 Fit side-chains REVERT: A 60 LYS cc_start: 0.8497 (mttt) cc_final: 0.8094 (mttp) REVERT: A 96 LYS cc_start: 0.6322 (ttmt) cc_final: 0.5727 (tttp) REVERT: B 57 GLU cc_start: 0.8478 (pt0) cc_final: 0.8196 (pt0) REVERT: B 60 LYS cc_start: 0.8382 (mttt) cc_final: 0.7848 (mtpt) REVERT: B 96 LYS cc_start: 0.6512 (ttmt) cc_final: 0.5834 (tttm) REVERT: C 60 LYS cc_start: 0.8246 (mttt) cc_final: 0.7959 (mttp) REVERT: C 96 LYS cc_start: 0.5946 (ttmt) cc_final: 0.5504 (tttm) REVERT: D 60 LYS cc_start: 0.8287 (mttt) cc_final: 0.7862 (mttp) REVERT: D 96 LYS cc_start: 0.5437 (ttmt) cc_final: 0.4886 (tttp) REVERT: E 46 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7492 (mt-10) REVERT: E 57 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: E 94 PHE cc_start: 0.7729 (p90) cc_final: 0.7410 (p90) REVERT: E 96 LYS cc_start: 0.5171 (ttmt) cc_final: 0.4451 (tttp) REVERT: F 46 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7537 (mt-10) REVERT: F 60 LYS cc_start: 0.8309 (mttt) cc_final: 0.7937 (mttm) REVERT: F 94 PHE cc_start: 0.7833 (p90) cc_final: 0.7581 (p90) REVERT: F 96 LYS cc_start: 0.5297 (ttmt) cc_final: 0.4738 (tttp) REVERT: G 96 LYS cc_start: 0.4508 (ttmt) cc_final: 0.4041 (tttm) REVERT: H 60 LYS cc_start: 0.7808 (mttt) cc_final: 0.7373 (mttp) REVERT: H 96 LYS cc_start: 0.4972 (ttmt) cc_final: 0.4466 (tttm) REVERT: I 57 GLU cc_start: 0.8488 (pt0) cc_final: 0.8181 (pt0) REVERT: I 60 LYS cc_start: 0.8180 (mttt) cc_final: 0.7439 (tttm) REVERT: I 94 PHE cc_start: 0.7823 (p90) cc_final: 0.5040 (m-80) REVERT: I 96 LYS cc_start: 0.5272 (ttmt) cc_final: 0.4652 (tttp) REVERT: J 60 LYS cc_start: 0.8105 (mttt) cc_final: 0.7325 (tttp) REVERT: J 94 PHE cc_start: 0.7807 (p90) cc_final: 0.5267 (t80) REVERT: J 96 LYS cc_start: 0.5065 (ttmt) cc_final: 0.4561 (tttm) outliers start: 38 outliers final: 35 residues processed: 94 average time/residue: 1.0133 time to fit residues: 99.0052 Evaluate side-chains 109 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain C residue 49 VAL 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 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 46 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4729 r_free = 0.4729 target = 0.208992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.179395 restraints weight = 4403.285| |-----------------------------------------------------------------------------| r_work (start): 0.4481 rms_B_bonded: 2.58 r_work: 0.4390 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4279 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.4279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4080 Z= 0.296 Angle : 0.717 7.553 5510 Z= 0.425 Chirality : 0.057 0.253 720 Planarity : 0.003 0.022 680 Dihedral : 5.293 15.296 590 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 10.24 % Allowed : 16.83 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.007 HIS H 50 PHE 0.010 0.002 PHE C 94 TYR 0.005 0.001 TYR A 39 ********************** 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 111 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 0.466 Fit side-chains REVERT: A 60 LYS cc_start: 0.8565 (mttt) cc_final: 0.8081 (mttp) REVERT: A 96 LYS cc_start: 0.6313 (ttmt) cc_final: 0.5714 (tttp) REVERT: B 57 GLU cc_start: 0.8548 (pt0) cc_final: 0.8293 (pt0) REVERT: B 60 LYS cc_start: 0.8372 (mttt) cc_final: 0.7897 (mtpt) REVERT: B 96 LYS cc_start: 0.6582 (ttmt) cc_final: 0.5800 (tttm) REVERT: C 60 LYS cc_start: 0.8229 (mttt) cc_final: 0.7929 (mttp) REVERT: C 96 LYS cc_start: 0.5916 (ttmt) cc_final: 0.5476 (tttm) REVERT: D 60 LYS cc_start: 0.8336 (mttt) cc_final: 0.7918 (mttp) REVERT: D 94 PHE cc_start: 0.7684 (p90) cc_final: 0.7457 (p90) REVERT: D 96 LYS cc_start: 0.5365 (ttmt) cc_final: 0.4847 (tttp) REVERT: E 46 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7493 (mt-10) REVERT: E 57 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8409 (pt0) REVERT: E 60 LYS cc_start: 0.8366 (mttt) cc_final: 0.7814 (mtpt) REVERT: E 96 LYS cc_start: 0.5170 (ttmt) cc_final: 0.4526 (tttp) REVERT: F 46 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7666 (mt-10) REVERT: F 60 LYS cc_start: 0.8298 (mttt) cc_final: 0.7745 (mtpt) REVERT: F 94 PHE cc_start: 0.7822 (p90) cc_final: 0.7491 (p90) REVERT: F 96 LYS cc_start: 0.5138 (ttmt) cc_final: 0.4562 (tttp) REVERT: G 96 LYS cc_start: 0.4523 (ttmt) cc_final: 0.4079 (tttm) REVERT: H 60 LYS cc_start: 0.7852 (mttt) cc_final: 0.7412 (mttp) REVERT: H 96 LYS cc_start: 0.4888 (ttmt) cc_final: 0.4381 (tttm) REVERT: I 57 GLU cc_start: 0.8470 (pt0) cc_final: 0.8243 (pt0) REVERT: I 60 LYS cc_start: 0.8131 (mttt) cc_final: 0.7413 (tttm) REVERT: I 94 PHE cc_start: 0.7890 (p90) cc_final: 0.5052 (m-80) REVERT: I 96 LYS cc_start: 0.5040 (ttmt) cc_final: 0.4478 (tttp) REVERT: J 60 LYS cc_start: 0.8029 (mttt) cc_final: 0.7344 (tttp) REVERT: J 94 PHE cc_start: 0.7823 (p90) cc_final: 0.5385 (t80) REVERT: J 96 LYS cc_start: 0.4967 (ttmt) cc_final: 0.4503 (tttm) outliers start: 42 outliers final: 36 residues processed: 93 average time/residue: 0.9227 time to fit residues: 89.5244 Evaluate side-chains 108 residues out of total 410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 70 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 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 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 46 GLU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.4859 r_free = 0.4859 target = 0.223943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.194839 restraints weight = 4270.018| |-----------------------------------------------------------------------------| r_work (start): 0.4639 rms_B_bonded: 2.64 r_work: 0.4548 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4435 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 4080 Z= 0.140 Angle : 0.565 6.130 5510 Z= 0.336 Chirality : 0.053 0.200 720 Planarity : 0.003 0.020 680 Dihedral : 4.545 16.697 590 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 8.29 % Allowed : 18.54 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.29), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.22), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.005 HIS H 50 PHE 0.012 0.002 PHE C 94 TYR 0.003 0.001 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.54 seconds wall clock time: 57 minutes 11.14 seconds (3431.14 seconds total)