Starting phenix.real_space_refine on Mon Sep 23 16:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/09_2024/6osl_20185.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/09_2024/6osl_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/09_2024/6osl_20185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/09_2024/6osl_20185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/09_2024/6osl_20185.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osl_20185/09_2024/6osl_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 1.57, per 1000 atoms: 0.39 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: 0.92 Conformation dependent library (CDL) restraints added in 525.3 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: 0.79 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: 1.07 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.000 Find NCS groups from input model: 0.150 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.442 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: 1.1720 time to fit residues: 116.1639 Evaluate side-chains 68 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 fitting. rotamer outliers: 30 poor density : 78 time to evaluate : 0.434 Fit side-chains REVERT: A 57 GLU cc_start: 0.8068 (pt0) cc_final: 0.7780 (pt0) REVERT: A 60 LYS cc_start: 0.8450 (mttt) cc_final: 0.8026 (mttp) REVERT: A 96 LYS cc_start: 0.5966 (ttmt) cc_final: 0.5400 (tttp) REVERT: B 60 LYS cc_start: 0.8160 (mttt) cc_final: 0.7823 (mtpt) REVERT: B 96 LYS cc_start: 0.6441 (ttmt) cc_final: 0.5786 (tttm) REVERT: C 45 LYS cc_start: 0.6926 (pttt) cc_final: 0.6429 (ptpt) REVERT: C 60 LYS cc_start: 0.8145 (mttt) cc_final: 0.7838 (mttm) REVERT: C 96 LYS cc_start: 0.5838 (ttmt) cc_final: 0.5171 (tttm) REVERT: D 45 LYS cc_start: 0.7074 (pttt) cc_final: 0.6801 (ptpt) REVERT: D 60 LYS cc_start: 0.8206 (mttt) cc_final: 0.7924 (mttp) REVERT: D 94 PHE cc_start: 0.7562 (p90) cc_final: 0.7195 (p90) REVERT: D 96 LYS cc_start: 0.5719 (ttmt) cc_final: 0.5253 (tttm) REVERT: E 57 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: E 60 LYS cc_start: 0.8362 (mttt) cc_final: 0.7859 (mtpt) REVERT: E 94 PHE cc_start: 0.7686 (p90) cc_final: 0.7376 (p90) REVERT: E 96 LYS cc_start: 0.5427 (ttmt) cc_final: 0.4742 (tttp) REVERT: F 60 LYS cc_start: 0.8220 (mttt) cc_final: 0.7734 (mtpt) REVERT: F 94 PHE cc_start: 0.7563 (p90) cc_final: 0.7163 (p90) REVERT: F 96 LYS cc_start: 0.5751 (ttmt) cc_final: 0.5162 (tttp) REVERT: G 96 LYS cc_start: 0.4789 (ttmt) cc_final: 0.4379 (tttm) REVERT: H 60 LYS cc_start: 0.7865 (mttt) cc_final: 0.7499 (mttp) REVERT: H 96 LYS cc_start: 0.5308 (ttmt) cc_final: 0.4853 (tttp) REVERT: I 60 LYS cc_start: 0.8129 (mttt) cc_final: 0.7534 (tttm) REVERT: I 94 PHE cc_start: 0.7657 (p90) cc_final: 0.5217 (m-80) REVERT: I 96 LYS cc_start: 0.5699 (ttmt) cc_final: 0.5140 (tttp) REVERT: J 60 LYS cc_start: 0.7874 (mttt) cc_final: 0.7429 (tttm) REVERT: J 94 PHE cc_start: 0.7743 (p90) cc_final: 0.5436 (t80) REVERT: J 96 LYS cc_start: 0.5315 (ttmt) cc_final: 0.4909 (tttm) outliers start: 30 outliers final: 18 residues processed: 87 average time/residue: 1.1477 time to fit residues: 103.0965 Evaluate side-chains 90 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 25 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 44 optimal weight: 0.0270 overall best weight: 2.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4080 Z= 0.182 Angle : 0.631 6.842 5510 Z= 0.378 Chirality : 0.057 0.222 720 Planarity : 0.003 0.016 680 Dihedral : 4.903 14.929 590 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 8.78 % Allowed : 18.54 % 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: -3.57 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.007 HIS H 50 PHE 0.020 0.003 PHE C 94 TYR 0.002 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 121 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 85 time to evaluate : 0.462 Fit side-chains REVERT: A 57 GLU cc_start: 0.7896 (pt0) cc_final: 0.7472 (pt0) REVERT: A 60 LYS cc_start: 0.8418 (mttt) cc_final: 0.7992 (mttp) REVERT: A 96 LYS cc_start: 0.6004 (ttmt) cc_final: 0.5434 (tttp) REVERT: B 45 LYS cc_start: 0.6730 (pttt) cc_final: 0.6509 (ptpt) REVERT: B 60 LYS cc_start: 0.8167 (mttt) cc_final: 0.7797 (mtpt) REVERT: B 96 LYS cc_start: 0.6585 (ttmt) cc_final: 0.5903 (tttm) REVERT: C 45 LYS cc_start: 0.6691 (pttt) cc_final: 0.6345 (ptmt) REVERT: C 60 LYS cc_start: 0.8085 (mttt) cc_final: 0.7790 (mttp) REVERT: C 96 LYS cc_start: 0.5775 (ttmt) cc_final: 0.5159 (tttm) REVERT: D 60 LYS cc_start: 0.8173 (mttt) cc_final: 0.7885 (mttp) REVERT: D 94 PHE cc_start: 0.7576 (p90) cc_final: 0.7251 (p90) REVERT: D 96 LYS cc_start: 0.5567 (ttmt) cc_final: 0.5090 (tttm) REVERT: E 57 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8255 (pt0) REVERT: E 60 LYS cc_start: 0.8237 (mttt) cc_final: 0.7727 (mtpt) REVERT: E 94 PHE cc_start: 0.7595 (p90) cc_final: 0.7289 (p90) REVERT: E 96 LYS cc_start: 0.5359 (ttmt) cc_final: 0.4645 (tttp) REVERT: F 60 LYS cc_start: 0.8186 (mttt) cc_final: 0.7673 (mtpt) REVERT: F 94 PHE cc_start: 0.7537 (p90) cc_final: 0.7204 (p90) REVERT: F 96 LYS cc_start: 0.5810 (ttmt) cc_final: 0.5220 (tttp) REVERT: G 96 LYS cc_start: 0.4784 (ttmt) cc_final: 0.4365 (tttm) REVERT: H 60 LYS cc_start: 0.7828 (mttt) cc_final: 0.7465 (mttp) REVERT: H 96 LYS cc_start: 0.5367 (ttmt) cc_final: 0.4900 (tttm) REVERT: I 60 LYS cc_start: 0.8044 (mttt) cc_final: 0.7459 (tttm) REVERT: I 94 PHE cc_start: 0.7559 (p90) cc_final: 0.5155 (m-80) REVERT: I 96 LYS cc_start: 0.5760 (ttmt) cc_final: 0.5198 (tttp) REVERT: J 60 LYS cc_start: 0.7802 (mttt) cc_final: 0.7426 (tttm) REVERT: J 94 PHE cc_start: 0.7713 (p90) cc_final: 0.5384 (t80) REVERT: J 96 LYS cc_start: 0.5315 (ttmt) cc_final: 0.4890 (tttm) outliers start: 36 outliers final: 24 residues processed: 99 average time/residue: 0.9476 time to fit residues: 97.4973 Evaluate side-chains 94 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 69 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B 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 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 81 THR Chi-restraints excluded: chain E residue 92 THR 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 92 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 5 optimal weight: 30.0000 chunk 21 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4080 Z= 0.362 Angle : 0.776 8.395 5510 Z= 0.460 Chirality : 0.060 0.277 720 Planarity : 0.003 0.018 680 Dihedral : 5.550 15.468 590 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 11.46 % Allowed : 15.12 % 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: -3.55 (0.26), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.016 0.009 HIS H 50 PHE 0.010 0.002 PHE C 94 TYR 0.006 0.001 TYR A 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 114 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 67 time to evaluate : 0.458 Fit side-chains REVERT: A 57 GLU cc_start: 0.8018 (pt0) cc_final: 0.7753 (pt0) REVERT: A 60 LYS cc_start: 0.8374 (mttt) cc_final: 0.7952 (mttp) REVERT: A 96 LYS cc_start: 0.6087 (ttmt) cc_final: 0.5526 (tttp) REVERT: B 45 LYS cc_start: 0.7050 (pttt) cc_final: 0.6755 (ptpt) REVERT: B 60 LYS cc_start: 0.8057 (mttt) cc_final: 0.7728 (mtpt) REVERT: B 96 LYS cc_start: 0.6522 (ttmt) cc_final: 0.5855 (tttm) REVERT: C 45 LYS cc_start: 0.6678 (pttt) cc_final: 0.6341 (ptmt) REVERT: C 60 LYS cc_start: 0.8059 (mttt) cc_final: 0.7751 (mttp) REVERT: C 96 LYS cc_start: 0.5820 (ttmt) cc_final: 0.5263 (tttm) REVERT: D 60 LYS cc_start: 0.8099 (mttt) cc_final: 0.7810 (mttp) REVERT: D 94 PHE cc_start: 0.7540 (p90) cc_final: 0.7228 (p90) REVERT: D 96 LYS cc_start: 0.5651 (ttmt) cc_final: 0.5210 (tttm) REVERT: E 57 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: E 60 LYS cc_start: 0.8221 (mttt) cc_final: 0.7680 (mtpt) REVERT: E 94 PHE cc_start: 0.7703 (p90) cc_final: 0.7402 (p90) REVERT: E 96 LYS cc_start: 0.5481 (ttmt) cc_final: 0.4747 (tttp) REVERT: F 45 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7092 (ptpt) REVERT: F 60 LYS cc_start: 0.8158 (mttt) cc_final: 0.7647 (mtpt) REVERT: F 94 PHE cc_start: 0.7560 (p90) cc_final: 0.7294 (p90) REVERT: F 96 LYS cc_start: 0.5761 (ttmt) cc_final: 0.5190 (tttp) REVERT: G 96 LYS cc_start: 0.4833 (ttmt) cc_final: 0.4423 (tttm) REVERT: H 60 LYS cc_start: 0.7829 (mttt) cc_final: 0.7459 (mttp) REVERT: H 96 LYS cc_start: 0.5289 (ttmt) cc_final: 0.4819 (tttp) REVERT: I 60 LYS cc_start: 0.8091 (mttt) cc_final: 0.7496 (tttp) REVERT: I 94 PHE cc_start: 0.7669 (p90) cc_final: 0.5231 (m-80) REVERT: I 96 LYS cc_start: 0.5594 (ttmt) cc_final: 0.5022 (tttp) REVERT: J 60 LYS cc_start: 0.7822 (mttt) cc_final: 0.7461 (tttm) REVERT: J 94 PHE cc_start: 0.7483 (p90) cc_final: 0.5334 (t80) REVERT: J 96 LYS cc_start: 0.5327 (ttmt) cc_final: 0.4816 (tmtm) outliers start: 47 outliers final: 40 residues processed: 93 average time/residue: 1.0198 time to fit residues: 98.3593 Evaluate side-chains 108 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 66 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 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 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 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4080 Z= 0.170 Angle : 0.600 6.248 5510 Z= 0.358 Chirality : 0.055 0.225 720 Planarity : 0.003 0.016 680 Dihedral : 4.813 16.373 590 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -3.32 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.006 HIS H 50 PHE 0.010 0.002 PHE C 94 TYR 0.003 0.001 TYR C 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 125 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 79 time to evaluate : 0.460 Fit side-chains REVERT: A 60 LYS cc_start: 0.8305 (mttt) cc_final: 0.7902 (mttp) REVERT: A 96 LYS cc_start: 0.6427 (ttmt) cc_final: 0.5782 (tttp) REVERT: B 60 LYS cc_start: 0.8080 (mttt) cc_final: 0.7694 (mtpt) REVERT: B 96 LYS cc_start: 0.6571 (ttmt) cc_final: 0.5889 (tttm) REVERT: C 45 LYS cc_start: 0.6504 (pttt) cc_final: 0.6154 (ptmt) REVERT: C 60 LYS cc_start: 0.8016 (mttt) cc_final: 0.7721 (mttm) REVERT: C 96 LYS cc_start: 0.5683 (ttmt) cc_final: 0.5303 (tttm) REVERT: D 60 LYS cc_start: 0.8071 (mttt) cc_final: 0.7757 (mttp) REVERT: D 94 PHE cc_start: 0.7440 (p90) cc_final: 0.7161 (p90) REVERT: D 96 LYS cc_start: 0.5638 (ttmt) cc_final: 0.5170 (tttm) REVERT: E 57 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8228 (pt0) REVERT: E 60 LYS cc_start: 0.8178 (mttt) cc_final: 0.7687 (mtpt) REVERT: E 94 PHE cc_start: 0.7526 (p90) cc_final: 0.7221 (p90) REVERT: E 96 LYS cc_start: 0.5507 (ttmt) cc_final: 0.4806 (tttp) REVERT: F 45 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6964 (ptpt) REVERT: F 46 GLU cc_start: 0.7439 (mt-10) cc_final: 0.6936 (mt-10) REVERT: F 60 LYS cc_start: 0.8167 (mttt) cc_final: 0.7791 (mttm) REVERT: F 94 PHE cc_start: 0.7511 (p90) cc_final: 0.7302 (p90) REVERT: F 96 LYS cc_start: 0.5825 (ttmt) cc_final: 0.5264 (tttp) REVERT: G 96 LYS cc_start: 0.4772 (ttmt) cc_final: 0.4352 (tttm) REVERT: H 60 LYS cc_start: 0.7726 (mttt) cc_final: 0.7376 (mttp) REVERT: H 96 LYS cc_start: 0.5279 (ttmt) cc_final: 0.4832 (tttm) REVERT: I 60 LYS cc_start: 0.7939 (mttt) cc_final: 0.7400 (tttm) REVERT: I 94 PHE cc_start: 0.7597 (p90) cc_final: 0.5192 (m-80) REVERT: I 96 LYS cc_start: 0.5753 (ttmt) cc_final: 0.5155 (tttp) REVERT: J 60 LYS cc_start: 0.7784 (mttt) cc_final: 0.7404 (tttm) REVERT: J 94 PHE cc_start: 0.7530 (p90) cc_final: 0.5363 (t80) REVERT: J 96 LYS cc_start: 0.5329 (ttmt) cc_final: 0.4889 (tttm) outliers start: 46 outliers final: 38 residues processed: 104 average time/residue: 0.9244 time to fit residues: 99.9796 Evaluate side-chains 109 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 69 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 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 49 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 20.0000 chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4080 Z= 0.278 Angle : 0.695 7.462 5510 Z= 0.412 Chirality : 0.057 0.257 720 Planarity : 0.003 0.016 680 Dihedral : 5.210 15.230 590 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 11.95 % Allowed : 14.88 % 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: -3.32 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.007 HIS H 50 PHE 0.007 0.001 PHE F 94 TYR 0.005 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 121 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 72 time to evaluate : 0.468 Fit side-chains REVERT: A 60 LYS cc_start: 0.8308 (mttt) cc_final: 0.7898 (mttp) REVERT: A 96 LYS cc_start: 0.6427 (ttmt) cc_final: 0.5795 (tttp) REVERT: B 60 LYS cc_start: 0.8020 (mttt) cc_final: 0.7696 (mtpt) REVERT: B 96 LYS cc_start: 0.6579 (ttmt) cc_final: 0.5899 (tttm) REVERT: C 60 LYS cc_start: 0.8035 (mttt) cc_final: 0.7734 (mttp) REVERT: C 96 LYS cc_start: 0.5710 (ttmt) cc_final: 0.5379 (tttm) REVERT: D 60 LYS cc_start: 0.8084 (mttt) cc_final: 0.7771 (mttp) REVERT: D 94 PHE cc_start: 0.7523 (p90) cc_final: 0.7258 (p90) REVERT: D 96 LYS cc_start: 0.5705 (ttmt) cc_final: 0.5198 (tttm) REVERT: E 57 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8060 (pt0) REVERT: E 60 LYS cc_start: 0.8167 (mttt) cc_final: 0.7664 (mtpt) REVERT: E 94 PHE cc_start: 0.7680 (p90) cc_final: 0.7370 (p90) REVERT: E 96 LYS cc_start: 0.5499 (ttmt) cc_final: 0.4808 (tttp) REVERT: F 45 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.6996 (ptpt) REVERT: F 46 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7193 (mt-10) REVERT: F 60 LYS cc_start: 0.8150 (mttt) cc_final: 0.7640 (mtpt) REVERT: F 96 LYS cc_start: 0.5725 (ttmt) cc_final: 0.5167 (tttp) REVERT: G 96 LYS cc_start: 0.4771 (ttmt) cc_final: 0.4342 (tttm) REVERT: H 60 LYS cc_start: 0.7751 (mttt) cc_final: 0.7391 (mttp) REVERT: H 96 LYS cc_start: 0.5216 (ttmt) cc_final: 0.4774 (tttm) REVERT: I 60 LYS cc_start: 0.8039 (mttt) cc_final: 0.7472 (tttm) REVERT: I 94 PHE cc_start: 0.7651 (p90) cc_final: 0.5147 (m-80) REVERT: I 96 LYS cc_start: 0.5451 (ttmt) cc_final: 0.4849 (tttp) REVERT: J 60 LYS cc_start: 0.7822 (mttt) cc_final: 0.7424 (tttm) REVERT: J 94 PHE cc_start: 0.7554 (p90) cc_final: 0.5392 (t80) REVERT: J 96 LYS cc_start: 0.5316 (ttmt) cc_final: 0.4802 (tmtm) outliers start: 49 outliers final: 41 residues processed: 99 average time/residue: 0.9048 time to fit residues: 93.4240 Evaluate side-chains 112 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 69 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 57 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 48 optimal weight: 0.0020 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4080 Z= 0.349 Angle : 0.760 8.149 5510 Z= 0.449 Chirality : 0.059 0.278 720 Planarity : 0.003 0.017 680 Dihedral : 5.509 16.024 590 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 12.20 % Allowed : 14.88 % 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: -3.41 (0.26), 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 0.015 0.008 HIS F 50 PHE 0.018 0.002 PHE F 94 TYR 0.006 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 119 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 69 time to evaluate : 0.455 Fit side-chains REVERT: A 60 LYS cc_start: 0.8361 (mttt) cc_final: 0.7958 (mttp) REVERT: A 96 LYS cc_start: 0.6431 (ttmt) cc_final: 0.5800 (tttp) REVERT: B 45 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.6897 (ptpt) REVERT: B 60 LYS cc_start: 0.8026 (mttt) cc_final: 0.7705 (mtpt) REVERT: B 96 LYS cc_start: 0.6577 (ttmt) cc_final: 0.5885 (tttm) REVERT: C 60 LYS cc_start: 0.8050 (mttt) cc_final: 0.7745 (mttm) REVERT: C 96 LYS cc_start: 0.5725 (ttmt) cc_final: 0.5403 (tttm) REVERT: D 60 LYS cc_start: 0.8103 (mttt) cc_final: 0.7792 (mttp) REVERT: D 96 LYS cc_start: 0.5580 (ttmt) cc_final: 0.5175 (tttm) REVERT: E 57 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: E 60 LYS cc_start: 0.8183 (mttt) cc_final: 0.7679 (mtpt) REVERT: E 96 LYS cc_start: 0.5511 (ttmt) cc_final: 0.4852 (tttp) REVERT: F 45 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7056 (ptpt) REVERT: F 46 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7198 (mt-10) REVERT: F 60 LYS cc_start: 0.8144 (mttt) cc_final: 0.7648 (mtpt) REVERT: F 96 LYS cc_start: 0.5588 (ttmt) cc_final: 0.5110 (tttp) REVERT: G 96 LYS cc_start: 0.4747 (ttmt) cc_final: 0.4323 (tttm) REVERT: H 60 LYS cc_start: 0.7769 (mttt) cc_final: 0.7407 (mttp) REVERT: H 96 LYS cc_start: 0.5363 (ttmt) cc_final: 0.4888 (tttm) REVERT: I 60 LYS cc_start: 0.8073 (mttt) cc_final: 0.7475 (tttm) REVERT: I 94 PHE cc_start: 0.7706 (p90) cc_final: 0.5149 (m-80) REVERT: I 96 LYS cc_start: 0.5512 (ttmt) cc_final: 0.4959 (tttp) REVERT: J 60 LYS cc_start: 0.7837 (mttt) cc_final: 0.7418 (tttm) REVERT: J 94 PHE cc_start: 0.7466 (p90) cc_final: 0.5347 (t80) REVERT: J 96 LYS cc_start: 0.5269 (ttmt) cc_final: 0.4777 (tmtm) outliers start: 50 outliers final: 43 residues processed: 97 average time/residue: 0.9309 time to fit residues: 94.1003 Evaluate side-chains 113 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 67 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 45 LYS Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 54 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 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 chunk 35 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4080 Z= 0.276 Angle : 0.694 7.310 5510 Z= 0.412 Chirality : 0.057 0.257 720 Planarity : 0.003 0.016 680 Dihedral : 5.283 18.550 590 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 12.20 % Allowed : 14.88 % 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: -3.32 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.014 0.008 HIS F 50 PHE 0.017 0.002 PHE D 94 TYR 0.005 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 123 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 73 time to evaluate : 0.388 Fit side-chains REVERT: A 60 LYS cc_start: 0.8372 (mttt) cc_final: 0.7964 (mttp) REVERT: A 96 LYS cc_start: 0.6415 (ttmt) cc_final: 0.5813 (tttp) REVERT: B 60 LYS cc_start: 0.8021 (mttt) cc_final: 0.7704 (mtpt) REVERT: B 96 LYS cc_start: 0.6578 (ttmt) cc_final: 0.5882 (tttm) REVERT: C 60 LYS cc_start: 0.8049 (mttt) cc_final: 0.7746 (mttp) REVERT: C 96 LYS cc_start: 0.5711 (ttmt) cc_final: 0.5390 (tttm) REVERT: D 60 LYS cc_start: 0.8095 (mttt) cc_final: 0.7773 (mttp) REVERT: D 96 LYS cc_start: 0.5556 (ttmt) cc_final: 0.5123 (tttm) REVERT: E 60 LYS cc_start: 0.8167 (mttt) cc_final: 0.7672 (mtpt) REVERT: E 96 LYS cc_start: 0.5455 (ttmt) cc_final: 0.4819 (tttp) REVERT: F 45 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6967 (ptpt) REVERT: F 60 LYS cc_start: 0.8154 (mttt) cc_final: 0.7662 (mtpt) REVERT: F 96 LYS cc_start: 0.5594 (ttmt) cc_final: 0.5124 (tttp) REVERT: G 96 LYS cc_start: 0.4746 (ttmt) cc_final: 0.4319 (tttm) REVERT: H 60 LYS cc_start: 0.7675 (mttt) cc_final: 0.7344 (mttp) REVERT: H 96 LYS cc_start: 0.5308 (ttmt) cc_final: 0.4835 (tttm) REVERT: I 60 LYS cc_start: 0.8053 (mttt) cc_final: 0.7473 (tttm) REVERT: I 94 PHE cc_start: 0.7666 (p90) cc_final: 0.5134 (m-80) REVERT: I 96 LYS cc_start: 0.5474 (ttmt) cc_final: 0.4913 (tttp) REVERT: J 60 LYS cc_start: 0.7830 (mttt) cc_final: 0.7417 (tttm) REVERT: J 94 PHE cc_start: 0.7557 (p90) cc_final: 0.5334 (t80) REVERT: J 96 LYS cc_start: 0.5354 (ttmt) cc_final: 0.4945 (tttm) outliers start: 50 outliers final: 43 residues processed: 99 average time/residue: 0.8841 time to fit residues: 91.2184 Evaluate side-chains 112 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 68 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4080 Z= 0.408 Angle : 0.801 8.495 5510 Z= 0.473 Chirality : 0.061 0.288 720 Planarity : 0.004 0.016 680 Dihedral : 5.798 20.560 590 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 11.71 % Allowed : 15.12 % 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: -3.40 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.20), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.008 HIS F 50 PHE 0.016 0.002 PHE D 94 TYR 0.007 0.001 TYR A 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 115 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 67 time to evaluate : 0.439 Fit side-chains REVERT: A 60 LYS cc_start: 0.8322 (mttt) cc_final: 0.7901 (mttp) REVERT: A 96 LYS cc_start: 0.6444 (ttmt) cc_final: 0.5862 (tttp) REVERT: B 60 LYS cc_start: 0.8051 (mttt) cc_final: 0.7725 (mtpt) REVERT: B 96 LYS cc_start: 0.6528 (ttmt) cc_final: 0.5879 (tttm) REVERT: C 60 LYS cc_start: 0.8068 (mttt) cc_final: 0.7757 (mttp) REVERT: C 96 LYS cc_start: 0.5737 (ttmt) cc_final: 0.5425 (tttm) REVERT: D 60 LYS cc_start: 0.8117 (mttt) cc_final: 0.7804 (mttp) REVERT: D 96 LYS cc_start: 0.5639 (ttmt) cc_final: 0.5140 (tttm) REVERT: E 60 LYS cc_start: 0.8207 (mttt) cc_final: 0.7696 (mtpt) REVERT: E 96 LYS cc_start: 0.5349 (ttmt) cc_final: 0.4766 (tttp) REVERT: F 45 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7088 (ptpt) REVERT: F 60 LYS cc_start: 0.8165 (mttt) cc_final: 0.7667 (mtpt) REVERT: F 96 LYS cc_start: 0.5435 (ttmt) cc_final: 0.4948 (tttp) REVERT: G 96 LYS cc_start: 0.4901 (ttmt) cc_final: 0.4461 (tttm) REVERT: H 60 LYS cc_start: 0.7771 (mttt) cc_final: 0.7403 (mttp) REVERT: H 96 LYS cc_start: 0.5433 (ttmt) cc_final: 0.4929 (tttm) REVERT: I 60 LYS cc_start: 0.8101 (mttt) cc_final: 0.7503 (tttm) REVERT: I 94 PHE cc_start: 0.7676 (p90) cc_final: 0.5065 (m-80) REVERT: I 96 LYS cc_start: 0.5529 (ttmt) cc_final: 0.4955 (tttp) REVERT: J 60 LYS cc_start: 0.7874 (mttt) cc_final: 0.7440 (tttm) REVERT: J 94 PHE cc_start: 0.7614 (p90) cc_final: 0.5367 (t80) REVERT: J 96 LYS cc_start: 0.5232 (ttmt) cc_final: 0.4850 (tttm) outliers start: 48 outliers final: 44 residues processed: 95 average time/residue: 0.9425 time to fit residues: 93.1220 Evaluate side-chains 111 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 66 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 72 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 57 GLU Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4080 Z= 0.172 Angle : 0.610 6.372 5510 Z= 0.363 Chirality : 0.054 0.220 720 Planarity : 0.003 0.016 680 Dihedral : 4.987 17.385 590 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 10.49 % Allowed : 16.83 % 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: -3.17 (0.28), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.006 HIS H 50 PHE 0.016 0.002 PHE F 94 TYR 0.004 0.001 TYR C 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 120 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 77 time to evaluate : 0.473 Fit side-chains REVERT: A 60 LYS cc_start: 0.8308 (mttt) cc_final: 0.7911 (mttp) REVERT: A 96 LYS cc_start: 0.6379 (ttmt) cc_final: 0.5772 (tttp) REVERT: B 60 LYS cc_start: 0.8108 (mttt) cc_final: 0.7715 (mtpt) REVERT: B 96 LYS cc_start: 0.6602 (ttmt) cc_final: 0.5936 (tttm) REVERT: C 60 LYS cc_start: 0.8025 (mttt) cc_final: 0.7739 (mttm) REVERT: C 96 LYS cc_start: 0.5723 (ttmt) cc_final: 0.5404 (tttm) REVERT: D 60 LYS cc_start: 0.8094 (mttt) cc_final: 0.7761 (mttp) REVERT: D 96 LYS cc_start: 0.5849 (ttmt) cc_final: 0.5337 (tttp) REVERT: E 57 GLU cc_start: 0.8286 (pt0) cc_final: 0.7932 (pt0) REVERT: E 60 LYS cc_start: 0.8145 (mttt) cc_final: 0.7657 (mtpt) REVERT: E 96 LYS cc_start: 0.5449 (ttmt) cc_final: 0.4845 (tttp) REVERT: F 45 LYS cc_start: 0.7167 (OUTLIER) cc_final: 0.6614 (ptpt) REVERT: F 60 LYS cc_start: 0.8175 (mttt) cc_final: 0.7794 (mttp) REVERT: F 96 LYS cc_start: 0.5488 (ttmt) cc_final: 0.4977 (tttp) REVERT: G 96 LYS cc_start: 0.4845 (ttmt) cc_final: 0.4408 (tttm) REVERT: H 60 LYS cc_start: 0.7608 (mttt) cc_final: 0.7284 (mttp) REVERT: H 96 LYS cc_start: 0.5306 (ttmt) cc_final: 0.4865 (tttm) REVERT: I 57 GLU cc_start: 0.8082 (pt0) cc_final: 0.7824 (pt0) REVERT: I 60 LYS cc_start: 0.7934 (mttt) cc_final: 0.7399 (tttm) REVERT: I 94 PHE cc_start: 0.7577 (p90) cc_final: 0.5039 (m-80) REVERT: I 96 LYS cc_start: 0.5566 (ttmt) cc_final: 0.5071 (tttp) REVERT: J 60 LYS cc_start: 0.7791 (mttt) cc_final: 0.7409 (tttp) REVERT: J 94 PHE cc_start: 0.7630 (p90) cc_final: 0.5324 (t80) REVERT: J 96 LYS cc_start: 0.5442 (ttmt) cc_final: 0.5027 (tttm) outliers start: 43 outliers final: 37 residues processed: 103 average time/residue: 0.8956 time to fit residues: 96.1581 Evaluate side-chains 111 residues out of total 410 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 73 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 92 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 49 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 81 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 20.0000 chunk 5 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- 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 = 0.4699 r_free = 0.4699 target = 0.202617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.173481 restraints weight = 4430.040| |-----------------------------------------------------------------------------| r_work (start): 0.4446 rms_B_bonded: 2.55 r_work: 0.4352 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4241 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 4080 Z= 0.411 Angle : 0.812 8.896 5510 Z= 0.480 Chirality : 0.062 0.285 720 Planarity : 0.004 0.017 680 Dihedral : 5.859 20.391 590 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 10.00 % Allowed : 17.07 % 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: -3.31 (0.27), residues: 570 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.21), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.008 HIS F 50 PHE 0.019 0.002 PHE D 94 TYR 0.007 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1934.12 seconds wall clock time: 37 minutes 53.91 seconds (2273.91 seconds total)