Starting phenix.real_space_refine on Wed Feb 12 08:34:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a4l_15148/02_2025/8a4l_15148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a4l_15148/02_2025/8a4l_15148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8a4l_15148/02_2025/8a4l_15148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a4l_15148/02_2025/8a4l_15148.map" model { file = "/net/cci-nas-00/data/ceres_data/8a4l_15148/02_2025/8a4l_15148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a4l_15148/02_2025/8a4l_15148.cif" } resolution = 2.68 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= 0.002 sd= 0.015 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 4845 2.51 5 N 1350 2.21 5 O 1560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7755 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 517 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Chain breaks: 1 Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J, M, L, O, P Time building chain proxies: 2.39, per 1000 atoms: 0.31 Number of scatterers: 7755 At special positions: 0 Unit cell: (145.95, 141.75, 43.05, 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 1560 8.00 N 1350 7.00 C 4845 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: 1.75 Conformation dependent library (CDL) restraints added in 1.2 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 21 sheets defined 0.0% alpha, 61.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.083A pdb=" N LYS A 34 " --> pdb=" O GLU B 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS B 34 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS C 34 " --> pdb=" O GLU D 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS D 34 " --> pdb=" O GLU E 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 49 removed outlier: 6.808A pdb=" N TYR B 39 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL A 40 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY B 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER A 42 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS B 43 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR A 44 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS B 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR C 39 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 40 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY C 41 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER B 42 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS C 43 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS C 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR D 39 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C 40 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY D 41 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER C 42 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS D 43 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR C 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS D 45 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR E 39 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 40 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY E 41 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER D 42 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS E 43 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR D 44 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS E 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 53 through 57 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 72 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 79 Processing sheet with id=AA7, first strand: chain 'A' and resid 85 through 92 Processing sheet with id=AA8, first strand: chain 'F' and resid 15 through 23 Processing sheet with id=AA9, first strand: chain 'F' and resid 34 through 35 removed outlier: 6.083A pdb=" N LYS F 34 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS G 34 " --> pdb=" O GLU H 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS H 34 " --> pdb=" O GLU I 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 38 through 49 removed outlier: 6.808A pdb=" N TYR G 39 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL F 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY G 41 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER F 42 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS G 43 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR F 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS G 45 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR H 39 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 40 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY H 41 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER G 42 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS H 43 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR G 44 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS H 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR I 39 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL H 40 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY I 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER H 42 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS I 43 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR H 44 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS I 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR J 39 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL I 40 " --> pdb=" O TYR J 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY J 41 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER I 42 " --> pdb=" O GLY J 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS J 43 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR I 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS J 45 " --> pdb=" O THR I 44 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AB3, first strand: chain 'F' and resid 61 through 72 Processing sheet with id=AB4, first strand: chain 'F' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'F' and resid 85 through 92 Processing sheet with id=AB6, first strand: chain 'K' and resid 15 through 23 Processing sheet with id=AB7, first strand: chain 'K' and resid 34 through 35 removed outlier: 6.082A pdb=" N LYS K 34 " --> pdb=" O GLU L 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS L 34 " --> pdb=" O GLU M 35 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LYS M 34 " --> pdb=" O GLU O 35 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N LYS O 34 " --> pdb=" O GLU P 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'K' and resid 38 through 49 removed outlier: 6.808A pdb=" N TYR L 39 " --> pdb=" O LEU K 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL K 40 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY L 41 " --> pdb=" O VAL K 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER K 42 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS L 43 " --> pdb=" O SER K 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR K 44 " --> pdb=" O LYS L 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS L 45 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR M 39 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL L 40 " --> pdb=" O TYR M 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY M 41 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER L 42 " --> pdb=" O GLY M 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS M 43 " --> pdb=" O SER L 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR L 44 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS M 45 " --> pdb=" O THR L 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR O 39 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL M 40 " --> pdb=" O TYR O 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY O 41 " --> pdb=" O VAL M 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER M 42 " --> pdb=" O GLY O 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS O 43 " --> pdb=" O SER M 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR M 44 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS O 45 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR P 39 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL O 40 " --> pdb=" O TYR P 39 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY P 41 " --> pdb=" O VAL O 40 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N SER O 42 " --> pdb=" O GLY P 41 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LYS P 43 " --> pdb=" O SER O 42 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR O 44 " --> pdb=" O LYS P 43 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS P 45 " --> pdb=" O THR O 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 53 through 57 Processing sheet with id=AC1, first strand: chain 'K' and resid 61 through 72 Processing sheet with id=AC2, first strand: chain 'K' and resid 75 through 79 Processing sheet with id=AC3, first strand: chain 'K' and resid 85 through 92 456 hydrogen bonds defined for protein. 1368 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: 2.50 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1365 1.29 - 1.35: 1199 1.35 - 1.42: 256 1.42 - 1.48: 1281 1.48 - 1.54: 3669 Bond restraints: 7770 Sorted by residual: bond pdb=" CB THR H 72 " pdb=" CG2 THR H 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB THR A 72 " pdb=" CG2 THR A 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.49e+00 bond pdb=" CB THR E 72 " pdb=" CG2 THR E 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB THR C 72 " pdb=" CG2 THR C 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 bond pdb=" CB THR F 72 " pdb=" CG2 THR F 72 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.48e+00 ... (remaining 7765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 9862 1.19 - 2.38: 518 2.38 - 3.57: 45 3.57 - 4.77: 15 4.77 - 5.96: 30 Bond angle restraints: 10470 Sorted by residual: angle pdb=" CA GLU H 61 " pdb=" CB GLU H 61 " pdb=" CG GLU H 61 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" CA GLU O 61 " pdb=" CB GLU O 61 " pdb=" CG GLU O 61 " ideal model delta sigma weight residual 114.10 120.06 -5.96 2.00e+00 2.50e-01 8.87e+00 angle pdb=" CA GLU D 61 " pdb=" CB GLU D 61 " pdb=" CG GLU D 61 " ideal model delta sigma weight residual 114.10 120.04 -5.94 2.00e+00 2.50e-01 8.83e+00 angle pdb=" CA GLU M 61 " pdb=" CB GLU M 61 " pdb=" CG GLU M 61 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.80e+00 angle pdb=" CA GLU A 61 " pdb=" CB GLU A 61 " pdb=" CG GLU A 61 " ideal model delta sigma weight residual 114.10 120.03 -5.93 2.00e+00 2.50e-01 8.78e+00 ... (remaining 10465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.30: 4260 15.30 - 30.60: 180 30.60 - 45.91: 90 45.91 - 61.21: 30 61.21 - 76.51: 15 Dihedral angle restraints: 4575 sinusoidal: 1545 harmonic: 3030 Sorted by residual: dihedral pdb=" CA LYS E 60 " pdb=" C LYS E 60 " pdb=" N GLU E 61 " pdb=" CA GLU E 61 " ideal model delta harmonic sigma weight residual -180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA LYS I 60 " pdb=" C LYS I 60 " pdb=" N GLU I 61 " pdb=" CA GLU I 61 " ideal model delta harmonic sigma weight residual 180.00 -155.23 -24.77 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA LYS C 60 " pdb=" C LYS C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta harmonic sigma weight residual -180.00 -155.24 -24.76 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 4572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 718 0.032 - 0.065: 358 0.065 - 0.097: 139 0.097 - 0.130: 150 0.130 - 0.162: 15 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CB THR A 72 " pdb=" CA THR A 72 " pdb=" OG1 THR A 72 " pdb=" CG2 THR A 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" CB THR H 72 " pdb=" CA THR H 72 " pdb=" OG1 THR H 72 " pdb=" CG2 THR H 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB THR B 72 " pdb=" CA THR B 72 " pdb=" OG1 THR B 72 " pdb=" CG2 THR B 72 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1377 not shown) Planarity restraints: 1290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 73 " 0.003 2.00e-02 2.50e+03 6.21e-03 3.85e-01 pdb=" C GLY B 73 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY B 73 " 0.004 2.00e-02 2.50e+03 pdb=" N VAL B 74 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY O 73 " -0.003 2.00e-02 2.50e+03 6.18e-03 3.82e-01 pdb=" C GLY O 73 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY O 73 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL O 74 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY G 73 " -0.003 2.00e-02 2.50e+03 6.18e-03 3.81e-01 pdb=" C GLY G 73 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY G 73 " -0.004 2.00e-02 2.50e+03 pdb=" N VAL G 74 " -0.004 2.00e-02 2.50e+03 ... (remaining 1287 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 2667 2.89 - 3.39: 6455 3.39 - 3.89: 13223 3.89 - 4.40: 15272 4.40 - 4.90: 28140 Nonbonded interactions: 65757 Sorted by model distance: nonbonded pdb=" OE2 GLU D 35 " pdb=" NZ LYS D 80 " model vdw 2.385 3.120 nonbonded pdb=" OE2 GLU P 35 " pdb=" NZ LYS P 80 " model vdw 2.385 3.120 nonbonded pdb=" OE2 GLU O 35 " pdb=" NZ LYS O 80 " model vdw 2.385 3.120 nonbonded pdb=" OE2 GLU G 35 " pdb=" NZ LYS G 80 " model vdw 2.385 3.120 nonbonded pdb=" OE2 GLU F 35 " pdb=" NZ LYS F 80 " model vdw 2.385 3.120 ... (remaining 65752 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'P' } 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 18.970 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:12.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 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 : 0.004 0.040 7770 Z= 0.255 Angle : 0.646 5.957 10470 Z= 0.369 Chirality : 0.053 0.162 1380 Planarity : 0.001 0.006 1290 Dihedral : 13.435 76.508 2655 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -3.33 (0.22), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.17), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS J 50 PHE 0.007 0.003 PHE O 94 TYR 0.009 0.002 TYR O 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.801 Fit side-chains REVERT: G 35 GLU cc_start: 0.7564 (tm-30) cc_final: 0.6896 (tm-30) REVERT: I 35 GLU cc_start: 0.7426 (tm-30) cc_final: 0.6821 (tm-30) REVERT: J 23 LYS cc_start: 0.7913 (ttmt) cc_final: 0.7572 (ttmm) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 1.6189 time to fit residues: 300.1902 Evaluate side-chains 141 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN F 65 ASN H 65 ASN I 65 ASN K 65 ASN L 65 ASN M 65 ASN O 65 ASN P 65 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.108105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.089115 restraints weight = 9363.050| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.25 r_work: 0.3242 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.066 7770 Z= 0.620 Angle : 0.731 7.807 10470 Z= 0.397 Chirality : 0.059 0.184 1380 Planarity : 0.003 0.009 1290 Dihedral : 5.755 28.208 1110 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.05 % Allowed : 14.23 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS J 50 PHE 0.014 0.003 PHE O 94 TYR 0.008 0.002 TYR P 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 0.830 Fit side-chains REVERT: A 46 GLU cc_start: 0.8523 (tt0) cc_final: 0.8024 (tm-30) REVERT: B 33 THR cc_start: 0.7399 (t) cc_final: 0.7196 (t) REVERT: B 46 GLU cc_start: 0.8504 (tt0) cc_final: 0.7929 (tm-30) REVERT: C 20 GLU cc_start: 0.8258 (mp0) cc_final: 0.7961 (mp0) REVERT: C 46 GLU cc_start: 0.8516 (tt0) cc_final: 0.8181 (tm-30) REVERT: D 35 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7144 (tm-30) REVERT: D 45 LYS cc_start: 0.8818 (tttm) cc_final: 0.8591 (tttm) REVERT: D 57 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7912 (mt-10) REVERT: D 65 ASN cc_start: 0.9167 (OUTLIER) cc_final: 0.8817 (t0) REVERT: E 35 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7673 (tm-30) REVERT: F 46 GLU cc_start: 0.8489 (tt0) cc_final: 0.8086 (tm-30) REVERT: H 35 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7098 (tm-30) REVERT: I 35 GLU cc_start: 0.8256 (tm-30) cc_final: 0.7359 (tm-30) REVERT: K 61 GLU cc_start: 0.6384 (tm-30) cc_final: 0.6088 (mt-10) REVERT: L 58 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8882 (mttt) REVERT: M 42 SER cc_start: 0.8789 (t) cc_final: 0.8583 (t) REVERT: O 35 GLU cc_start: 0.8201 (tm-30) cc_final: 0.7204 (tm-30) REVERT: P 42 SER cc_start: 0.8884 (t) cc_final: 0.8556 (m) outliers start: 16 outliers final: 6 residues processed: 196 average time/residue: 1.6634 time to fit residues: 339.6894 Evaluate side-chains 193 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 185 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 GLN Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 42 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN G 65 ASN I 65 ASN L 65 ASN O 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091111 restraints weight = 9377.998| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.24 r_work: 0.3301 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3176 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7770 Z= 0.356 Angle : 0.574 7.379 10470 Z= 0.312 Chirality : 0.054 0.138 1380 Planarity : 0.002 0.008 1290 Dihedral : 5.165 23.576 1110 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.97 % Allowed : 18.08 % Favored : 77.95 % 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: -3.63 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS H 50 PHE 0.012 0.002 PHE G 94 TYR 0.007 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.849 Fit side-chains REVERT: A 46 GLU cc_start: 0.8495 (tt0) cc_final: 0.8056 (tm-30) REVERT: B 33 THR cc_start: 0.7440 (t) cc_final: 0.7209 (t) REVERT: B 34 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7658 (mtpt) REVERT: B 46 GLU cc_start: 0.8500 (tt0) cc_final: 0.7932 (tm-30) REVERT: C 20 GLU cc_start: 0.8241 (mp0) cc_final: 0.8001 (mp0) REVERT: C 46 GLU cc_start: 0.8471 (tt0) cc_final: 0.8160 (tm-30) REVERT: D 35 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7220 (tm-30) REVERT: D 57 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7925 (mt-10) REVERT: D 65 ASN cc_start: 0.9133 (t0) cc_final: 0.8865 (t0) REVERT: E 35 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7898 (tm-30) REVERT: F 46 GLU cc_start: 0.8448 (tt0) cc_final: 0.8071 (tm-30) REVERT: H 35 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7155 (tm-30) REVERT: I 35 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7247 (tm-30) REVERT: J 35 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7157 (tm-30) REVERT: L 58 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8878 (mttt) REVERT: O 33 THR cc_start: 0.7125 (t) cc_final: 0.6779 (t) REVERT: P 42 SER cc_start: 0.8844 (t) cc_final: 0.8544 (m) outliers start: 31 outliers final: 17 residues processed: 195 average time/residue: 1.5424 time to fit residues: 314.1775 Evaluate side-chains 188 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 19 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 89 optimal weight: 10.0000 chunk 64 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 65 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN G 65 ASN I 65 ASN L 65 ASN P 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.106488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.087629 restraints weight = 9494.779| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.21 r_work: 0.3247 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 7770 Z= 0.555 Angle : 0.664 9.058 10470 Z= 0.364 Chirality : 0.057 0.167 1380 Planarity : 0.003 0.008 1290 Dihedral : 5.421 23.471 1110 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.13 % Allowed : 18.33 % Favored : 76.54 % 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: -3.68 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS A 50 PHE 0.014 0.003 PHE G 94 TYR 0.008 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 184 time to evaluate : 0.799 Fit side-chains REVERT: A 46 GLU cc_start: 0.8471 (tt0) cc_final: 0.8062 (tm-30) REVERT: B 33 THR cc_start: 0.7507 (t) cc_final: 0.7302 (t) REVERT: B 34 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7659 (mtpt) REVERT: B 46 GLU cc_start: 0.8526 (tt0) cc_final: 0.7973 (tm-30) REVERT: C 20 GLU cc_start: 0.8271 (mp0) cc_final: 0.8027 (mp0) REVERT: C 46 GLU cc_start: 0.8488 (tt0) cc_final: 0.8194 (tm-30) REVERT: D 33 THR cc_start: 0.7258 (OUTLIER) cc_final: 0.6909 (t) REVERT: D 65 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8717 (t0) REVERT: F 46 GLU cc_start: 0.8488 (tt0) cc_final: 0.8114 (tm-30) REVERT: G 35 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7304 (tm-30) REVERT: H 35 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7341 (tm-30) REVERT: I 35 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7306 (tm-30) REVERT: J 35 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7259 (tm-30) REVERT: K 46 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: M 33 THR cc_start: 0.7141 (OUTLIER) cc_final: 0.6874 (t) REVERT: O 33 THR cc_start: 0.7229 (t) cc_final: 0.6795 (t) REVERT: P 42 SER cc_start: 0.8878 (t) cc_final: 0.8580 (m) outliers start: 40 outliers final: 20 residues processed: 206 average time/residue: 1.4787 time to fit residues: 318.4161 Evaluate side-chains 202 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 24 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN L 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.107519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.088726 restraints weight = 9342.865| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.22 r_work: 0.3267 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 7770 Z= 0.485 Angle : 0.627 9.673 10470 Z= 0.344 Chirality : 0.056 0.151 1380 Planarity : 0.002 0.008 1290 Dihedral : 5.230 20.083 1110 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.51 % Allowed : 18.59 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.69 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 50 PHE 0.013 0.003 PHE O 94 TYR 0.009 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.826 Fit side-chains REVERT: A 46 GLU cc_start: 0.8474 (tt0) cc_final: 0.8044 (tm-30) REVERT: B 33 THR cc_start: 0.7432 (t) cc_final: 0.7204 (t) REVERT: B 46 GLU cc_start: 0.8514 (tt0) cc_final: 0.7951 (tm-30) REVERT: C 20 GLU cc_start: 0.8256 (mp0) cc_final: 0.8046 (mp0) REVERT: C 46 GLU cc_start: 0.8506 (tt0) cc_final: 0.8212 (tm-30) REVERT: D 33 THR cc_start: 0.7330 (OUTLIER) cc_final: 0.6985 (t) REVERT: F 46 GLU cc_start: 0.8485 (tt0) cc_final: 0.8104 (tm-30) REVERT: G 35 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7310 (tm-30) REVERT: H 35 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7375 (tm-30) REVERT: I 33 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6798 (t) REVERT: I 35 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7296 (tm-30) REVERT: J 35 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7293 (tm-30) REVERT: K 46 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: L 58 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8913 (mttt) REVERT: M 33 THR cc_start: 0.7294 (OUTLIER) cc_final: 0.6998 (t) REVERT: O 33 THR cc_start: 0.7239 (OUTLIER) cc_final: 0.6778 (t) REVERT: P 24 GLN cc_start: 0.6431 (mp10) cc_final: 0.5523 (mp10) REVERT: P 42 SER cc_start: 0.8874 (t) cc_final: 0.8577 (m) outliers start: 43 outliers final: 23 residues processed: 203 average time/residue: 1.4293 time to fit residues: 303.7920 Evaluate side-chains 205 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 24 GLN Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.108306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.089651 restraints weight = 9326.878| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.21 r_work: 0.3267 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 7770 Z= 0.419 Angle : 0.596 9.082 10470 Z= 0.326 Chirality : 0.055 0.140 1380 Planarity : 0.002 0.008 1290 Dihedral : 5.066 17.338 1110 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.13 % Allowed : 19.10 % Favored : 75.77 % 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: -3.67 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS A 50 PHE 0.012 0.003 PHE O 94 TYR 0.012 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.815 Fit side-chains REVERT: A 46 GLU cc_start: 0.8447 (tt0) cc_final: 0.8055 (tm-30) REVERT: B 33 THR cc_start: 0.7258 (t) cc_final: 0.7014 (t) REVERT: B 46 GLU cc_start: 0.8509 (tt0) cc_final: 0.7902 (tm-30) REVERT: C 20 GLU cc_start: 0.8275 (mp0) cc_final: 0.7939 (mp0) REVERT: C 46 GLU cc_start: 0.8465 (tt0) cc_final: 0.8159 (tm-30) REVERT: D 33 THR cc_start: 0.7279 (OUTLIER) cc_final: 0.6955 (t) REVERT: D 65 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8771 (t0) REVERT: F 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8058 (tm-30) REVERT: H 35 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7263 (tm-30) REVERT: I 33 THR cc_start: 0.7018 (OUTLIER) cc_final: 0.6772 (t) REVERT: I 35 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7256 (tm-30) REVERT: J 35 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7345 (tm-30) REVERT: K 46 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: L 58 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8816 (mttt) REVERT: M 33 THR cc_start: 0.7232 (OUTLIER) cc_final: 0.6919 (t) REVERT: O 33 THR cc_start: 0.7169 (OUTLIER) cc_final: 0.6732 (t) REVERT: P 42 SER cc_start: 0.8872 (t) cc_final: 0.8555 (m) outliers start: 40 outliers final: 24 residues processed: 193 average time/residue: 1.4244 time to fit residues: 287.7875 Evaluate side-chains 200 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 24 GLN Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.111493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.092884 restraints weight = 9234.208| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.20 r_work: 0.3322 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 7770 Z= 0.257 Angle : 0.526 9.138 10470 Z= 0.287 Chirality : 0.053 0.121 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.693 13.523 1110 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.87 % Allowed : 20.26 % Favored : 74.87 % 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: -3.63 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.010 0.002 PHE G 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 0.836 Fit side-chains REVERT: A 46 GLU cc_start: 0.8388 (tt0) cc_final: 0.8055 (tm-30) REVERT: A 61 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.5802 (mm-30) REVERT: B 33 THR cc_start: 0.7182 (t) cc_final: 0.6931 (t) REVERT: B 46 GLU cc_start: 0.8505 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 20 GLU cc_start: 0.8282 (mp0) cc_final: 0.7961 (mp0) REVERT: C 46 GLU cc_start: 0.8428 (tt0) cc_final: 0.8149 (tm-30) REVERT: D 33 THR cc_start: 0.7203 (OUTLIER) cc_final: 0.6828 (t) REVERT: D 65 ASN cc_start: 0.9065 (OUTLIER) cc_final: 0.8552 (t0) REVERT: F 46 GLU cc_start: 0.8440 (tt0) cc_final: 0.8069 (tm-30) REVERT: F 61 GLU cc_start: 0.6179 (OUTLIER) cc_final: 0.5574 (mm-30) REVERT: H 35 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7294 (tm-30) REVERT: I 33 THR cc_start: 0.7015 (OUTLIER) cc_final: 0.6753 (t) REVERT: I 35 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7309 (tm-30) REVERT: J 35 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7395 (tm-30) REVERT: K 46 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8143 (tt0) REVERT: K 61 GLU cc_start: 0.6085 (OUTLIER) cc_final: 0.5554 (mm-30) REVERT: L 58 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8709 (mttt) REVERT: M 33 THR cc_start: 0.7105 (OUTLIER) cc_final: 0.6769 (t) REVERT: O 33 THR cc_start: 0.7149 (OUTLIER) cc_final: 0.6696 (t) REVERT: P 42 SER cc_start: 0.8819 (t) cc_final: 0.8530 (m) outliers start: 38 outliers final: 22 residues processed: 186 average time/residue: 1.4634 time to fit residues: 285.6669 Evaluate side-chains 194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 46 GLU Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.107524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.088618 restraints weight = 9385.035| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.23 r_work: 0.3274 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.030 7770 Z= 0.465 Angle : 0.627 9.996 10470 Z= 0.343 Chirality : 0.056 0.151 1380 Planarity : 0.002 0.008 1290 Dihedral : 5.058 13.894 1110 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.74 % Allowed : 20.90 % Favored : 74.36 % 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: -3.68 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS A 50 PHE 0.013 0.003 PHE G 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 177 time to evaluate : 0.847 Fit side-chains REVERT: A 46 GLU cc_start: 0.8451 (tt0) cc_final: 0.8089 (tm-30) REVERT: B 33 THR cc_start: 0.7300 (t) cc_final: 0.7052 (t) REVERT: B 46 GLU cc_start: 0.8554 (tt0) cc_final: 0.7953 (tm-30) REVERT: C 20 GLU cc_start: 0.8312 (mp0) cc_final: 0.8025 (mp0) REVERT: C 46 GLU cc_start: 0.8476 (tt0) cc_final: 0.8197 (tm-30) REVERT: F 46 GLU cc_start: 0.8502 (tt0) cc_final: 0.8117 (tm-30) REVERT: F 61 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5618 (mm-30) REVERT: G 35 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7299 (tm-30) REVERT: H 35 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7402 (tm-30) REVERT: I 33 THR cc_start: 0.7049 (OUTLIER) cc_final: 0.6800 (t) REVERT: I 35 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7314 (tm-30) REVERT: J 35 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7399 (tm-30) REVERT: K 46 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: M 33 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6873 (t) REVERT: O 33 THR cc_start: 0.7187 (OUTLIER) cc_final: 0.6775 (t) REVERT: P 42 SER cc_start: 0.8889 (t) cc_final: 0.8594 (m) outliers start: 37 outliers final: 24 residues processed: 197 average time/residue: 1.4874 time to fit residues: 306.3604 Evaluate side-chains 204 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 175 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 45 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.109528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090783 restraints weight = 9384.575| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.24 r_work: 0.3296 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 7770 Z= 0.331 Angle : 0.570 9.378 10470 Z= 0.311 Chirality : 0.054 0.124 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.845 13.881 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.36 % Allowed : 21.67 % Favored : 73.97 % 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: -3.66 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS H 50 PHE 0.011 0.002 PHE G 94 TYR 0.011 0.002 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.882 Fit side-chains REVERT: A 46 GLU cc_start: 0.8433 (tt0) cc_final: 0.8089 (tm-30) REVERT: A 61 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5686 (mm-30) REVERT: B 33 THR cc_start: 0.7214 (t) cc_final: 0.6969 (t) REVERT: B 46 GLU cc_start: 0.8516 (tt0) cc_final: 0.7888 (tm-30) REVERT: C 20 GLU cc_start: 0.8318 (mp0) cc_final: 0.8033 (mp0) REVERT: C 46 GLU cc_start: 0.8450 (tt0) cc_final: 0.8173 (tm-30) REVERT: D 33 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.6907 (t) REVERT: D 65 ASN cc_start: 0.8972 (t0) cc_final: 0.8748 (t0) REVERT: F 46 GLU cc_start: 0.8462 (tt0) cc_final: 0.8080 (tm-30) REVERT: F 61 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.5586 (mm-30) REVERT: G 35 GLU cc_start: 0.8405 (tm-30) cc_final: 0.7288 (tm-30) REVERT: G 58 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8554 (mtpt) REVERT: H 35 GLU cc_start: 0.8203 (tm-30) cc_final: 0.7388 (tm-30) REVERT: I 33 THR cc_start: 0.6999 (OUTLIER) cc_final: 0.6758 (t) REVERT: I 35 GLU cc_start: 0.8327 (tm-30) cc_final: 0.7282 (tm-30) REVERT: J 35 GLU cc_start: 0.8346 (tm-30) cc_final: 0.7409 (tm-30) REVERT: K 46 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8127 (tt0) REVERT: L 58 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8730 (mttt) REVERT: M 33 THR cc_start: 0.7095 (OUTLIER) cc_final: 0.6781 (t) REVERT: O 33 THR cc_start: 0.7169 (OUTLIER) cc_final: 0.6762 (t) REVERT: P 42 SER cc_start: 0.8857 (t) cc_final: 0.8563 (m) outliers start: 34 outliers final: 22 residues processed: 182 average time/residue: 1.4585 time to fit residues: 278.1248 Evaluate side-chains 195 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 65 ASN L 65 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089731 restraints weight = 9389.187| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.21 r_work: 0.3274 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 7770 Z= 0.416 Angle : 0.617 9.812 10470 Z= 0.336 Chirality : 0.055 0.140 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.981 13.974 1110 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.74 % Allowed : 21.92 % Favored : 73.33 % 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: -3.68 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS J 50 PHE 0.012 0.003 PHE G 94 TYR 0.013 0.002 TYR I 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.834 Fit side-chains REVERT: A 46 GLU cc_start: 0.8433 (tt0) cc_final: 0.8067 (tm-30) REVERT: B 33 THR cc_start: 0.7271 (t) cc_final: 0.7015 (t) REVERT: B 46 GLU cc_start: 0.8535 (tt0) cc_final: 0.7923 (tm-30) REVERT: C 20 GLU cc_start: 0.8327 (mp0) cc_final: 0.8032 (mp0) REVERT: C 46 GLU cc_start: 0.8456 (tt0) cc_final: 0.8171 (tm-30) REVERT: D 33 THR cc_start: 0.7278 (OUTLIER) cc_final: 0.6956 (t) REVERT: F 46 GLU cc_start: 0.8478 (tt0) cc_final: 0.8095 (tm-30) REVERT: F 61 GLU cc_start: 0.6273 (OUTLIER) cc_final: 0.5591 (mm-30) REVERT: G 35 GLU cc_start: 0.8421 (tm-30) cc_final: 0.7261 (tm-30) REVERT: G 58 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8621 (mtpt) REVERT: H 35 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7403 (tm-30) REVERT: I 33 THR cc_start: 0.6994 (OUTLIER) cc_final: 0.6740 (t) REVERT: I 35 GLU cc_start: 0.8344 (tm-30) cc_final: 0.7289 (tm-30) REVERT: J 35 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7391 (tm-30) REVERT: K 46 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: K 61 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5411 (mm-30) REVERT: L 58 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8779 (mttt) REVERT: M 20 GLU cc_start: 0.8318 (mp0) cc_final: 0.8079 (mp0) REVERT: M 33 THR cc_start: 0.6975 (OUTLIER) cc_final: 0.6706 (t) REVERT: P 42 SER cc_start: 0.8882 (t) cc_final: 0.8584 (m) outliers start: 37 outliers final: 24 residues processed: 194 average time/residue: 1.4661 time to fit residues: 297.6970 Evaluate side-chains 205 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 58 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 61 GLU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 33 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 45 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 44 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 94 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 53 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.110712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.092057 restraints weight = 9259.416| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.22 r_work: 0.3311 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7770 Z= 0.295 Angle : 0.561 9.259 10470 Z= 0.304 Chirality : 0.053 0.121 1380 Planarity : 0.002 0.010 1290 Dihedral : 4.766 13.650 1110 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.10 % Allowed : 22.95 % Favored : 72.95 % 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: -3.64 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.010 0.002 PHE G 94 TYR 0.014 0.002 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6548.12 seconds wall clock time: 116 minutes 24.04 seconds (6984.04 seconds total)