Starting phenix.real_space_refine on Wed Mar 12 08:35:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a4l_15148/03_2025/8a4l_15148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a4l_15148/03_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_15148/03_2025/8a4l_15148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a4l_15148/03_2025/8a4l_15148.map" model { file = "/net/cci-nas-00/data/ceres_data/8a4l_15148/03_2025/8a4l_15148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a4l_15148/03_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-5624/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: 2.21, per 1000 atoms: 0.28 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: 1.72 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: 1.20 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: 2.28 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: 0.09 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: 0.900 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.610 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 : 0.814 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: 1.6188 time to fit residues: 299.9943 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 : 0.898 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.089130 restraints weight = 9363.050| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.25 r_work: 0.3252 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 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 : 0.923 Fit side-chains REVERT: A 46 GLU cc_start: 0.8532 (tt0) cc_final: 0.8060 (tm-30) REVERT: B 46 GLU cc_start: 0.8517 (tt0) cc_final: 0.7964 (tm-30) REVERT: C 20 GLU cc_start: 0.8258 (mp0) cc_final: 0.7971 (mp0) REVERT: C 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8207 (tm-30) REVERT: D 35 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7177 (tm-30) REVERT: D 45 LYS cc_start: 0.8849 (tttm) cc_final: 0.8628 (tttm) REVERT: D 57 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7924 (mt-10) REVERT: D 65 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8807 (t0) REVERT: E 35 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7712 (tm-30) REVERT: F 46 GLU cc_start: 0.8489 (tt0) cc_final: 0.8111 (tm-30) REVERT: H 35 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7120 (tm-30) REVERT: I 35 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7382 (tm-30) REVERT: K 61 GLU cc_start: 0.6410 (tm-30) cc_final: 0.6150 (mt-10) REVERT: L 58 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8909 (mttt) REVERT: M 42 SER cc_start: 0.8788 (t) cc_final: 0.8582 (t) REVERT: O 35 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7240 (tm-30) REVERT: P 42 SER cc_start: 0.8889 (t) cc_final: 0.8583 (m) outliers start: 16 outliers final: 6 residues processed: 196 average time/residue: 1.6408 time to fit residues: 334.8435 Evaluate side-chains 192 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 184 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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: 7.9990 chunk 79 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 82 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.3648 r_free = 0.3648 target = 0.109176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.090377 restraints weight = 9420.882| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.23 r_work: 0.3283 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 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 : 0.006 0.050 7770 Z= 0.408 Angle : 0.600 7.643 10470 Z= 0.326 Chirality : 0.055 0.139 1380 Planarity : 0.002 0.009 1290 Dihedral : 5.269 24.075 1110 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.36 % Allowed : 18.08 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 0.007 0.003 HIS J 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 216 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.900 Fit side-chains REVERT: A 46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8035 (tm-30) REVERT: B 34 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.7651 (mtpt) REVERT: B 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.7920 (tm-30) REVERT: C 20 GLU cc_start: 0.8272 (mp0) cc_final: 0.8010 (mp0) REVERT: C 46 GLU cc_start: 0.8470 (tt0) cc_final: 0.8155 (tm-30) REVERT: D 65 ASN cc_start: 0.9129 (t0) cc_final: 0.8896 (t0) REVERT: F 46 GLU cc_start: 0.8461 (tt0) cc_final: 0.8083 (tm-30) REVERT: G 65 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8847 (t0) REVERT: H 35 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7171 (tm-30) REVERT: I 33 THR cc_start: 0.6991 (t) cc_final: 0.6717 (t) REVERT: I 35 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7244 (tm-30) REVERT: J 35 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7131 (tm-30) REVERT: K 46 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: L 58 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8897 (mttt) REVERT: O 33 THR cc_start: 0.7221 (t) cc_final: 0.6911 (t) REVERT: P 42 SER cc_start: 0.8865 (t) cc_final: 0.8557 (m) outliers start: 34 outliers final: 17 residues processed: 198 average time/residue: 1.4823 time to fit residues: 306.5478 Evaluate side-chains 194 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 65 ASN 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 46 GLU 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: 7.9990 chunk 73 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 89 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 65 ASN I 65 ASN L 65 ASN P 65 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.087249 restraints weight = 9512.119| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.23 r_work: 0.3239 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 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 : 0.009 0.056 7770 Z= 0.589 Angle : 0.679 9.312 10470 Z= 0.373 Chirality : 0.058 0.171 1380 Planarity : 0.003 0.009 1290 Dihedral : 5.468 23.505 1110 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.13 % Allowed : 18.08 % Favored : 76.79 % 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 : -2.79 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS J 50 PHE 0.014 0.003 PHE G 94 TYR 0.009 0.002 TYR I 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 226 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 186 time to evaluate : 0.826 Fit side-chains REVERT: A 46 GLU cc_start: 0.8486 (tt0) cc_final: 0.8069 (tm-30) REVERT: B 34 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7682 (mtpt) REVERT: B 46 GLU cc_start: 0.8527 (tt0) cc_final: 0.7972 (tm-30) REVERT: C 20 GLU cc_start: 0.8281 (mp0) cc_final: 0.8018 (mp0) REVERT: C 46 GLU cc_start: 0.8500 (tt0) cc_final: 0.8201 (tm-30) REVERT: D 33 THR cc_start: 0.7360 (OUTLIER) cc_final: 0.7031 (t) REVERT: D 65 ASN cc_start: 0.9162 (t0) cc_final: 0.8819 (t0) REVERT: F 46 GLU cc_start: 0.8490 (tt0) cc_final: 0.8110 (tm-30) REVERT: G 35 GLU cc_start: 0.8379 (tm-30) cc_final: 0.7295 (tm-30) REVERT: H 35 GLU cc_start: 0.8108 (tm-30) cc_final: 0.7331 (tm-30) REVERT: I 35 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7279 (tm-30) REVERT: J 24 GLN cc_start: 0.6314 (mp10) cc_final: 0.5336 (mp10) REVERT: J 35 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7251 (tm-30) REVERT: K 46 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8084 (tt0) REVERT: M 33 THR cc_start: 0.7094 (OUTLIER) cc_final: 0.6829 (t) REVERT: O 33 THR cc_start: 0.7218 (t) cc_final: 0.6780 (t) REVERT: P 42 SER cc_start: 0.8885 (t) cc_final: 0.8585 (m) outliers start: 40 outliers final: 22 residues processed: 209 average time/residue: 1.5053 time to fit residues: 329.0593 Evaluate side-chains 208 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 33 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 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 46 GLU 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 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: 8.9990 chunk 10 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 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 = 0.3663 r_free = 0.3663 target = 0.109911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.091122 restraints weight = 9242.090| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.23 r_work: 0.3296 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 7770 Z= 0.323 Angle : 0.550 8.778 10470 Z= 0.300 Chirality : 0.054 0.122 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.912 18.420 1110 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.51 % Allowed : 18.21 % Favored : 76.28 % 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: -3.65 (0.19), 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 0.002 HIS H 50 PHE 0.011 0.002 PHE G 94 TYR 0.011 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 214 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 171 time to evaluate : 0.802 Fit side-chains REVERT: A 34 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8296 (mttt) REVERT: A 46 GLU cc_start: 0.8430 (tt0) cc_final: 0.8037 (tm-30) REVERT: B 46 GLU cc_start: 0.8509 (tt0) cc_final: 0.7928 (tm-30) REVERT: C 20 GLU cc_start: 0.8265 (mp0) cc_final: 0.7969 (mp0) REVERT: C 46 GLU cc_start: 0.8455 (tt0) cc_final: 0.8174 (tm-30) REVERT: D 33 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.6908 (t) REVERT: D 65 ASN cc_start: 0.9154 (t0) cc_final: 0.8851 (t0) REVERT: F 46 GLU cc_start: 0.8480 (tt0) cc_final: 0.8096 (tm-30) REVERT: H 35 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7281 (tm-30) REVERT: I 33 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6760 (t) REVERT: I 35 GLU cc_start: 0.8303 (tm-30) cc_final: 0.7324 (tm-30) REVERT: J 24 GLN cc_start: 0.6499 (mp10) cc_final: 0.6237 (mp10) REVERT: J 35 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7291 (tm-30) REVERT: K 46 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: L 58 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8832 (mttt) REVERT: M 33 THR cc_start: 0.7229 (OUTLIER) cc_final: 0.6928 (t) REVERT: O 33 THR cc_start: 0.7213 (OUTLIER) cc_final: 0.6738 (t) REVERT: P 42 SER cc_start: 0.8841 (t) cc_final: 0.8546 (m) outliers start: 43 outliers final: 21 residues processed: 197 average time/residue: 1.4620 time to fit residues: 300.8424 Evaluate side-chains 192 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 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 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 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: 10.0000 chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 44 optimal weight: 7.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 = 0.3637 r_free = 0.3637 target = 0.108170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.089422 restraints weight = 9346.753| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.20 r_work: 0.3273 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 7770 Z= 0.392 Angle : 0.587 9.754 10470 Z= 0.321 Chirality : 0.055 0.136 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.973 16.642 1110 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.51 % Allowed : 18.97 % Favored : 75.51 % 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 (0.19), 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 0.006 0.003 HIS A 50 PHE 0.012 0.003 PHE G 94 TYR 0.009 0.002 TYR C 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 212 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 169 time to evaluate : 0.939 Fit side-chains REVERT: A 46 GLU cc_start: 0.8444 (tt0) cc_final: 0.8043 (tm-30) REVERT: B 46 GLU cc_start: 0.8505 (tt0) cc_final: 0.7924 (tm-30) REVERT: C 20 GLU cc_start: 0.8271 (mp0) cc_final: 0.8052 (mp0) REVERT: C 46 GLU cc_start: 0.8452 (tt0) cc_final: 0.8160 (tm-30) REVERT: D 33 THR cc_start: 0.7345 (OUTLIER) cc_final: 0.6944 (t) REVERT: D 65 ASN cc_start: 0.9157 (t0) cc_final: 0.8854 (t0) REVERT: F 46 GLU cc_start: 0.8463 (tt0) cc_final: 0.8071 (tm-30) REVERT: H 35 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7294 (tm-30) REVERT: I 33 THR cc_start: 0.7081 (OUTLIER) cc_final: 0.6794 (t) REVERT: I 35 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7299 (tm-30) REVERT: J 24 GLN cc_start: 0.6663 (mp10) cc_final: 0.6447 (mp10) REVERT: J 35 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7314 (tm-30) REVERT: K 46 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: L 58 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8786 (mttt) REVERT: M 33 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6991 (t) REVERT: O 33 THR cc_start: 0.7149 (OUTLIER) cc_final: 0.6694 (t) REVERT: P 42 SER cc_start: 0.8877 (t) cc_final: 0.8581 (m) outliers start: 43 outliers final: 25 residues processed: 190 average time/residue: 1.4008 time to fit residues: 278.8543 Evaluate side-chains 196 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 33 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 24 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 65 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.3651 r_free = 0.3651 target = 0.109162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.090415 restraints weight = 9326.750| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.22 r_work: 0.3294 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 7770 Z= 0.365 Angle : 0.569 9.326 10470 Z= 0.311 Chirality : 0.054 0.130 1380 Planarity : 0.002 0.010 1290 Dihedral : 4.864 13.818 1110 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.87 % Allowed : 19.87 % Favored : 75.26 % 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: -3.65 (0.19), 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 A 50 PHE 0.011 0.003 PHE G 94 TYR 0.012 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 208 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.810 Fit side-chains REVERT: A 46 GLU cc_start: 0.8451 (tt0) cc_final: 0.8117 (tm-30) REVERT: B 46 GLU cc_start: 0.8565 (tt0) cc_final: 0.7975 (tm-30) REVERT: C 20 GLU cc_start: 0.8280 (mp0) cc_final: 0.7979 (mp0) REVERT: C 46 GLU cc_start: 0.8494 (tt0) cc_final: 0.8228 (tm-30) REVERT: D 33 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.7078 (t) REVERT: D 65 ASN cc_start: 0.9164 (t0) cc_final: 0.8830 (t0) REVERT: F 46 GLU cc_start: 0.8466 (tt0) cc_final: 0.8124 (tm-30) REVERT: F 61 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5634 (mm-30) REVERT: H 35 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7333 (tm-30) REVERT: I 33 THR cc_start: 0.7118 (OUTLIER) cc_final: 0.6865 (t) REVERT: I 35 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7324 (tm-30) REVERT: J 24 GLN cc_start: 0.6857 (mp10) cc_final: 0.6588 (mp10) REVERT: J 35 GLU cc_start: 0.8331 (tm-30) cc_final: 0.7413 (tm-30) REVERT: K 46 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: L 58 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8822 (mttt) REVERT: M 33 THR cc_start: 0.7140 (OUTLIER) cc_final: 0.6830 (t) REVERT: O 33 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6754 (t) REVERT: P 42 SER cc_start: 0.8871 (t) cc_final: 0.8598 (m) outliers start: 38 outliers final: 24 residues processed: 190 average time/residue: 1.4904 time to fit residues: 297.4104 Evaluate side-chains 196 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 33 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 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 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: 0.7980 chunk 23 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.112533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.093911 restraints weight = 9145.393| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.22 r_work: 0.3345 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7770 Z= 0.219 Angle : 0.512 8.911 10470 Z= 0.278 Chirality : 0.053 0.120 1380 Planarity : 0.002 0.014 1290 Dihedral : 4.535 13.085 1110 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.23 % Allowed : 20.90 % 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: -3.61 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE B 94 TYR 0.014 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 201 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 0.824 Fit side-chains REVERT: A 46 GLU cc_start: 0.8407 (tt0) cc_final: 0.8007 (tm-30) REVERT: A 61 GLU cc_start: 0.6310 (OUTLIER) cc_final: 0.5778 (mm-30) REVERT: A 72 THR cc_start: 0.9136 (OUTLIER) cc_final: 0.8842 (m) REVERT: B 46 GLU cc_start: 0.8508 (tt0) cc_final: 0.7878 (tm-30) REVERT: C 20 GLU cc_start: 0.8258 (mp0) cc_final: 0.7928 (mp0) REVERT: C 46 GLU cc_start: 0.8438 (tt0) cc_final: 0.8152 (tm-30) REVERT: D 33 THR cc_start: 0.7365 (OUTLIER) cc_final: 0.7024 (t) REVERT: D 65 ASN cc_start: 0.9126 (t0) cc_final: 0.8729 (t0) REVERT: F 46 GLU cc_start: 0.8432 (tt0) cc_final: 0.8064 (tm-30) REVERT: F 61 GLU cc_start: 0.6209 (OUTLIER) cc_final: 0.5621 (mm-30) REVERT: H 35 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7320 (tm-30) REVERT: I 33 THR cc_start: 0.6910 (OUTLIER) cc_final: 0.6634 (t) REVERT: I 35 GLU cc_start: 0.8353 (tm-30) cc_final: 0.7364 (tm-30) REVERT: J 35 GLU cc_start: 0.8334 (tm-30) cc_final: 0.7427 (tm-30) REVERT: K 61 GLU cc_start: 0.5940 (OUTLIER) cc_final: 0.5350 (mm-30) REVERT: L 58 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8662 (mttt) REVERT: M 33 THR cc_start: 0.7071 (OUTLIER) cc_final: 0.6740 (t) REVERT: O 33 THR cc_start: 0.7231 (OUTLIER) cc_final: 0.6774 (t) REVERT: P 42 SER cc_start: 0.8820 (t) cc_final: 0.8534 (m) outliers start: 33 outliers final: 17 residues processed: 185 average time/residue: 1.4510 time to fit residues: 280.6463 Evaluate side-chains 188 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain C residue 33 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 H residue 33 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 61 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 58 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 7 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 57 optimal weight: 8.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- 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 = 0.3630 r_free = 0.3630 target = 0.107797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.088926 restraints weight = 9467.782| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.24 r_work: 0.3268 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2890 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= 0.464 Angle : 0.622 9.832 10470 Z= 0.341 Chirality : 0.055 0.148 1380 Planarity : 0.003 0.014 1290 Dihedral : 4.996 13.657 1110 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.49 % Allowed : 20.64 % 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: -3.67 (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 0.007 0.004 HIS A 50 PHE 0.012 0.003 PHE G 94 TYR 0.016 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 212 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.693 Fit side-chains REVERT: A 46 GLU cc_start: 0.8460 (tt0) cc_final: 0.8104 (tm-30) REVERT: B 46 GLU cc_start: 0.8553 (tt0) cc_final: 0.7958 (tm-30) REVERT: C 20 GLU cc_start: 0.8289 (mp0) cc_final: 0.7937 (mp0) REVERT: C 46 GLU cc_start: 0.8493 (tt0) cc_final: 0.8208 (tm-30) REVERT: D 65 ASN cc_start: 0.9167 (t0) cc_final: 0.8840 (t0) REVERT: F 46 GLU cc_start: 0.8497 (tt0) cc_final: 0.8113 (tm-30) REVERT: F 61 GLU cc_start: 0.6295 (OUTLIER) cc_final: 0.5609 (mm-30) REVERT: G 35 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7317 (tm-30) REVERT: G 58 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8628 (mtpt) REVERT: H 35 GLU cc_start: 0.8180 (tm-30) cc_final: 0.7395 (tm-30) REVERT: I 33 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6781 (t) REVERT: I 35 GLU cc_start: 0.8335 (tm-30) cc_final: 0.7297 (tm-30) REVERT: J 35 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7376 (tm-30) REVERT: K 46 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: K 61 GLU cc_start: 0.6130 (OUTLIER) cc_final: 0.5463 (mm-30) REVERT: M 33 THR cc_start: 0.7053 (OUTLIER) cc_final: 0.6808 (t) REVERT: O 33 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6763 (t) REVERT: P 42 SER cc_start: 0.8892 (t) cc_final: 0.8593 (m) outliers start: 35 outliers final: 24 residues processed: 196 average time/residue: 1.5386 time to fit residues: 315.1185 Evaluate side-chains 206 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 33 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 24 GLN 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 46 GLU Chi-restraints excluded: chain K residue 61 GLU Chi-restraints excluded: chain L residue 33 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 78 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3675 r_free = 0.3675 target = 0.110751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.092064 restraints weight = 9230.176| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.21 r_work: 0.3322 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7770 Z= 0.276 Angle : 0.556 9.112 10470 Z= 0.302 Chirality : 0.053 0.120 1380 Planarity : 0.002 0.010 1290 Dihedral : 4.708 13.288 1110 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.10 % Allowed : 22.05 % Favored : 73.85 % 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 H 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 195 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.928 Fit side-chains REVERT: A 34 LYS cc_start: 0.8634 (mtpt) cc_final: 0.8337 (mttt) REVERT: A 46 GLU cc_start: 0.8430 (tt0) cc_final: 0.8048 (tm-30) REVERT: A 61 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5726 (mm-30) REVERT: B 46 GLU cc_start: 0.8520 (tt0) cc_final: 0.7893 (tm-30) REVERT: C 20 GLU cc_start: 0.8271 (mp0) cc_final: 0.7974 (mp0) REVERT: C 46 GLU cc_start: 0.8444 (tt0) cc_final: 0.8163 (tm-30) REVERT: D 33 THR cc_start: 0.7311 (OUTLIER) cc_final: 0.6968 (t) REVERT: D 65 ASN cc_start: 0.9144 (t0) cc_final: 0.8796 (t0) REVERT: F 46 GLU cc_start: 0.8453 (tt0) cc_final: 0.8091 (tm-30) REVERT: F 61 GLU cc_start: 0.6228 (OUTLIER) cc_final: 0.5605 (mm-30) REVERT: G 35 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7261 (tm-30) REVERT: G 58 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8599 (mtpt) REVERT: H 35 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7355 (tm-30) REVERT: I 33 THR cc_start: 0.6981 (OUTLIER) cc_final: 0.6715 (t) REVERT: I 35 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7240 (tm-30) REVERT: J 35 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7386 (tm-30) REVERT: K 61 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5361 (mm-30) REVERT: L 58 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8692 (mttt) REVERT: O 33 THR cc_start: 0.7138 (OUTLIER) cc_final: 0.6747 (t) REVERT: P 42 SER cc_start: 0.8845 (t) cc_final: 0.8555 (m) outliers start: 32 outliers final: 21 residues processed: 179 average time/residue: 1.7261 time to fit residues: 324.0254 Evaluate side-chains 191 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 33 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 61 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 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=1.00 ------------------------------------------------------------------------------- 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: 8.9990 chunk 96 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 57 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.107929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.089096 restraints weight = 9387.738| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.24 r_work: 0.3252 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.031 7770 Z= 0.456 Angle : 0.639 9.688 10470 Z= 0.348 Chirality : 0.055 0.147 1380 Planarity : 0.003 0.017 1290 Dihedral : 5.011 13.716 1110 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.62 % Allowed : 21.79 % Favored : 73.59 % 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 A 50 PHE 0.012 0.003 PHE O 94 TYR 0.017 0.003 TYR O 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7021.13 seconds wall clock time: 123 minutes 33.89 seconds (7413.89 seconds total)