Starting phenix.real_space_refine on Fri Aug 22 20:13:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a4l_15148/08_2025/8a4l_15148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a4l_15148/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8a4l_15148/08_2025/8a4l_15148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a4l_15148/08_2025/8a4l_15148.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a4l_15148/08_2025/8a4l_15148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a4l_15148/08_2025/8a4l_15148.map" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: B, C, D, E, F, G, H, I, J, K, L, M, O, P Time building chain proxies: 0.78, per 1000 atoms: 0.10 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: 0.38 Conformation dependent library (CDL) restraints added in 292.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.34 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: 1.19 Time building geometry restraints manager: 0.57 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.680 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.130 ------------------------------------------------------------------------------- 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= 0.191 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.009 0.002 TYR O 39 PHE 0.007 0.003 PHE O 94 HIS 0.003 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 7770) covalent geometry : angle 0.64619 (10470) hydrogen bonds : bond 0.10118 ( 456) hydrogen bonds : angle 6.32698 ( 1368) *********************** 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 : 0.182 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: 0.6716 time to fit residues: 124.5297 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 0.6980 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 6.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN E 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.090887 restraints weight = 9376.314| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.28 r_work: 0.3281 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 7770 Z= 0.341 Angle : 0.657 7.052 10470 Z= 0.356 Chirality : 0.056 0.156 1380 Planarity : 0.003 0.009 1290 Dihedral : 5.510 26.917 1110 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.92 % Allowed : 14.10 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR P 39 PHE 0.012 0.002 PHE O 94 HIS 0.007 0.004 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00728 ( 7770) covalent geometry : angle 0.65685 (10470) hydrogen bonds : bond 0.02936 ( 456) hydrogen bonds : angle 4.52743 ( 1368) *********************** 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 200 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 185 time to evaluate : 0.293 Fit side-chains REVERT: A 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.8051 (tm-30) REVERT: B 46 GLU cc_start: 0.8514 (tt0) cc_final: 0.7947 (tm-30) REVERT: C 20 GLU cc_start: 0.8277 (mp0) cc_final: 0.8041 (mp0) REVERT: C 46 GLU cc_start: 0.8529 (tt0) cc_final: 0.8189 (tm-30) REVERT: D 45 LYS cc_start: 0.8863 (tttm) cc_final: 0.8644 (tttm) REVERT: D 57 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7930 (mt-10) REVERT: D 65 ASN cc_start: 0.9141 (OUTLIER) cc_final: 0.8775 (t0) REVERT: E 35 GLU cc_start: 0.8120 (tm-30) cc_final: 0.7660 (tm-30) REVERT: L 58 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8893 (mttt) REVERT: O 24 GLN cc_start: 0.6485 (OUTLIER) cc_final: 0.6270 (mp10) REVERT: O 35 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7222 (tm-30) REVERT: P 42 SER cc_start: 0.8894 (t) cc_final: 0.8591 (m) outliers start: 15 outliers final: 5 residues processed: 188 average time/residue: 0.6821 time to fit residues: 133.6636 Evaluate side-chains 183 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 64 THR Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain O residue 24 GLN 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 12 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.112676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.093823 restraints weight = 9215.830| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.26 r_work: 0.3337 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2205 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= 0.196 Angle : 0.530 6.811 10470 Z= 0.287 Chirality : 0.053 0.135 1380 Planarity : 0.002 0.007 1290 Dihedral : 4.958 22.361 1110 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.33 % Allowed : 16.15 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.59 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.73 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR O 39 PHE 0.008 0.002 PHE O 94 HIS 0.004 0.002 HIS P 50 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7770) covalent geometry : angle 0.52958 (10470) hydrogen bonds : bond 0.01931 ( 456) hydrogen bonds : angle 4.18576 ( 1368) *********************** 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 199 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.288 Fit side-chains REVERT: A 46 GLU cc_start: 0.8503 (tt0) cc_final: 0.8052 (tm-30) REVERT: B 33 THR cc_start: 0.7412 (t) cc_final: 0.7195 (t) REVERT: B 34 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.7628 (mtpt) REVERT: B 46 GLU cc_start: 0.8525 (tt0) cc_final: 0.7931 (tm-30) REVERT: C 20 GLU cc_start: 0.8223 (mp0) cc_final: 0.8010 (mp0) REVERT: C 46 GLU cc_start: 0.8473 (tt0) cc_final: 0.8152 (tm-30) REVERT: D 57 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 65 ASN cc_start: 0.9139 (t0) cc_final: 0.8874 (t0) REVERT: E 35 GLU cc_start: 0.8184 (tm-30) cc_final: 0.7748 (tm-30) REVERT: F 46 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8118 (tm-30) REVERT: H 35 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7056 (tm-30) REVERT: I 35 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7270 (tm-30) REVERT: J 35 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7206 (tm-30) REVERT: K 46 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8188 (tt0) REVERT: L 58 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8816 (mttt) REVERT: P 42 SER cc_start: 0.8857 (t) cc_final: 0.8545 (m) outliers start: 26 outliers final: 10 residues processed: 182 average time/residue: 0.6636 time to fit residues: 125.7986 Evaluate side-chains 179 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 46 GLU 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 O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 56 optimal weight: 20.0000 chunk 45 optimal weight: 0.0980 chunk 73 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN D 65 ASN E 65 ASN G 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.090932 restraints weight = 9430.326| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.24 r_work: 0.3295 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7770 Z= 0.266 Angle : 0.569 8.139 10470 Z= 0.310 Chirality : 0.054 0.133 1380 Planarity : 0.002 0.007 1290 Dihedral : 5.045 21.581 1110 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.49 % Allowed : 19.10 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.011 0.002 TYR O 39 PHE 0.011 0.002 PHE O 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 7770) covalent geometry : angle 0.56861 (10470) hydrogen bonds : bond 0.02210 ( 456) hydrogen bonds : angle 4.25125 ( 1368) *********************** 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 212 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 177 time to evaluate : 0.180 Fit side-chains REVERT: A 46 GLU cc_start: 0.8498 (tt0) cc_final: 0.8039 (tm-30) REVERT: B 33 THR cc_start: 0.7423 (t) cc_final: 0.7159 (t) REVERT: B 34 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7635 (mtpt) REVERT: B 46 GLU cc_start: 0.8505 (tt0) cc_final: 0.7926 (tm-30) REVERT: C 20 GLU cc_start: 0.8224 (mp0) cc_final: 0.7959 (mp0) REVERT: C 46 GLU cc_start: 0.8456 (tt0) cc_final: 0.8145 (tm-30) REVERT: D 33 THR cc_start: 0.7419 (OUTLIER) cc_final: 0.7009 (t) REVERT: D 57 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7860 (mt-10) REVERT: D 65 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8699 (t0) REVERT: E 35 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7790 (tm-30) REVERT: F 46 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: G 35 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7256 (tm-30) REVERT: H 35 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7314 (tm-30) REVERT: I 33 THR cc_start: 0.7000 (t) cc_final: 0.6749 (t) REVERT: I 35 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7348 (tm-30) REVERT: I 61 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: J 35 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7219 (tm-30) REVERT: K 46 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: L 58 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8863 (mttt) REVERT: O 33 THR cc_start: 0.7244 (t) cc_final: 0.6932 (t) REVERT: O 35 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7204 (tm-30) REVERT: P 42 SER cc_start: 0.8879 (t) cc_final: 0.8572 (m) outliers start: 35 outliers final: 17 residues processed: 197 average time/residue: 0.6202 time to fit residues: 127.8062 Evaluate side-chains 196 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.277 ------------------------------------------------------------------------------- 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 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 46 GLU 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 61 GLU 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 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 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 10 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 83 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 0.0970 chunk 87 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.3665 r_free = 0.3665 target = 0.110529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.091703 restraints weight = 9364.148| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.25 r_work: 0.3302 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7770 Z= 0.226 Angle : 0.534 8.699 10470 Z= 0.292 Chirality : 0.053 0.121 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.835 18.548 1110 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.62 % Allowed : 19.23 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.010 0.002 TYR O 39 PHE 0.010 0.002 PHE O 94 HIS 0.005 0.003 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00470 ( 7770) covalent geometry : angle 0.53386 (10470) hydrogen bonds : bond 0.01952 ( 456) hydrogen bonds : angle 4.18393 ( 1368) *********************** 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 202 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.228 Fit side-chains REVERT: A 46 GLU cc_start: 0.8428 (tt0) cc_final: 0.8006 (tm-30) REVERT: B 33 THR cc_start: 0.7385 (t) cc_final: 0.7136 (t) REVERT: B 34 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7657 (mtpt) REVERT: B 46 GLU cc_start: 0.8492 (tt0) cc_final: 0.7919 (tm-30) REVERT: C 20 GLU cc_start: 0.8257 (mp0) cc_final: 0.7966 (mp0) REVERT: C 46 GLU cc_start: 0.8447 (tt0) cc_final: 0.8141 (tm-30) REVERT: D 33 THR cc_start: 0.7341 (OUTLIER) cc_final: 0.6925 (t) REVERT: D 35 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7296 (tm-30) REVERT: D 65 ASN cc_start: 0.9133 (t0) cc_final: 0.8931 (t0) REVERT: F 46 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: G 35 GLU cc_start: 0.8314 (tm-30) cc_final: 0.7202 (tm-30) REVERT: H 35 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7311 (tm-30) REVERT: I 33 THR cc_start: 0.6988 (t) cc_final: 0.6730 (t) REVERT: I 35 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7329 (tm-30) REVERT: J 35 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7270 (tm-30) REVERT: K 46 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8088 (tt0) REVERT: L 58 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8825 (mttt) REVERT: M 33 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6907 (t) REVERT: O 33 THR cc_start: 0.7107 (t) cc_final: 0.6603 (t) REVERT: P 42 SER cc_start: 0.8866 (t) cc_final: 0.8561 (m) outliers start: 36 outliers final: 18 residues processed: 188 average time/residue: 0.6099 time to fit residues: 119.8538 Evaluate side-chains 186 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 46 GLU 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 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 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 36 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 P 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.088429 restraints weight = 9495.133| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.24 r_work: 0.3260 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2727 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= 0.359 Angle : 0.624 10.026 10470 Z= 0.344 Chirality : 0.056 0.158 1380 Planarity : 0.003 0.008 1290 Dihedral : 5.130 20.320 1110 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.74 % Allowed : 18.21 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR O 39 PHE 0.013 0.003 PHE O 94 HIS 0.007 0.004 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00746 ( 7770) covalent geometry : angle 0.62438 (10470) hydrogen bonds : bond 0.02517 ( 456) hydrogen bonds : angle 4.40259 ( 1368) *********************** 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 217 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.222 Fit side-chains REVERT: A 34 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8264 (mttt) REVERT: A 46 GLU cc_start: 0.8469 (tt0) cc_final: 0.8049 (tm-30) REVERT: B 33 THR cc_start: 0.7488 (t) cc_final: 0.7262 (t) REVERT: B 34 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7687 (mtpt) REVERT: B 46 GLU cc_start: 0.8514 (tt0) cc_final: 0.7950 (tm-30) REVERT: C 20 GLU cc_start: 0.8237 (mp0) cc_final: 0.7999 (mp0) REVERT: C 46 GLU cc_start: 0.8489 (tt0) cc_final: 0.8188 (tm-30) REVERT: D 33 THR cc_start: 0.7281 (OUTLIER) cc_final: 0.6888 (t) REVERT: D 35 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7278 (tm-30) REVERT: D 65 ASN cc_start: 0.9180 (t0) cc_final: 0.8855 (t0) REVERT: E 35 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7880 (tm-30) REVERT: F 46 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: G 35 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7288 (tm-30) REVERT: H 35 GLU cc_start: 0.8177 (tm-30) cc_final: 0.7393 (tm-30) REVERT: I 33 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6855 (t) REVERT: I 35 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7306 (tm-30) REVERT: J 35 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7308 (tm-30) REVERT: K 46 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: L 42 SER cc_start: 0.8699 (t) cc_final: 0.8458 (p) REVERT: L 58 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8840 (mppt) REVERT: M 24 GLN cc_start: 0.6946 (mp10) cc_final: 0.6018 (mp10) REVERT: M 33 THR cc_start: 0.7180 (OUTLIER) cc_final: 0.6912 (t) REVERT: O 33 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6788 (t) REVERT: P 42 SER cc_start: 0.8875 (t) cc_final: 0.8575 (m) outliers start: 37 outliers final: 16 residues processed: 198 average time/residue: 0.6276 time to fit residues: 129.8139 Evaluate side-chains 199 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.259 ------------------------------------------------------------------------------- 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 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 46 GLU 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 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 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 35 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3671 r_free = 0.3671 target = 0.110888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.092124 restraints weight = 9300.334| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.23 r_work: 0.3311 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7770 Z= 0.200 Angle : 0.523 8.959 10470 Z= 0.286 Chirality : 0.053 0.121 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.689 14.529 1110 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.74 % Allowed : 19.10 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.64 (0.19), 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 TYR 0.008 0.002 TYR C 39 PHE 0.009 0.002 PHE O 94 HIS 0.004 0.002 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 7770) covalent geometry : angle 0.52345 (10470) hydrogen bonds : bond 0.01851 ( 456) hydrogen bonds : angle 4.17270 ( 1368) *********************** 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: 37 poor density : 167 time to evaluate : 0.276 Fit side-chains REVERT: A 34 LYS cc_start: 0.8605 (mtpt) cc_final: 0.8402 (mttt) REVERT: A 46 GLU cc_start: 0.8442 (tt0) cc_final: 0.8023 (tm-30) REVERT: B 33 THR cc_start: 0.7362 (t) cc_final: 0.7132 (t) REVERT: B 34 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.7656 (mtpt) REVERT: B 46 GLU cc_start: 0.8478 (tt0) cc_final: 0.7909 (tm-30) REVERT: C 20 GLU cc_start: 0.8281 (mp0) cc_final: 0.7965 (mp0) REVERT: C 46 GLU cc_start: 0.8427 (tt0) cc_final: 0.8144 (tm-30) REVERT: D 33 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.6937 (t) REVERT: D 35 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7318 (tm-30) REVERT: D 65 ASN cc_start: 0.9147 (t0) cc_final: 0.8802 (t0) REVERT: F 46 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8063 (tm-30) REVERT: F 61 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5608 (mm-30) REVERT: G 35 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7276 (tm-30) REVERT: H 35 GLU cc_start: 0.8158 (tm-30) cc_final: 0.7368 (tm-30) REVERT: I 33 THR cc_start: 0.6949 (OUTLIER) cc_final: 0.6676 (t) REVERT: I 35 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7305 (tm-30) REVERT: J 35 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7324 (tm-30) REVERT: K 46 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8122 (tt0) REVERT: L 58 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8753 (mttt) REVERT: M 33 THR cc_start: 0.7107 (OUTLIER) cc_final: 0.6800 (t) REVERT: M 34 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8146 (mtpt) REVERT: O 33 THR cc_start: 0.7153 (OUTLIER) cc_final: 0.6704 (t) REVERT: P 42 SER cc_start: 0.8830 (t) cc_final: 0.8538 (m) outliers start: 37 outliers final: 19 residues processed: 187 average time/residue: 0.6410 time to fit residues: 125.3795 Evaluate side-chains 192 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 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 46 GLU Chi-restraints excluded: chain F residue 61 GLU 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.107745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.088966 restraints weight = 9403.432| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.21 r_work: 0.3256 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2833 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= 0.327 Angle : 0.610 9.823 10470 Z= 0.335 Chirality : 0.055 0.147 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.985 14.037 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.62 % Allowed : 20.64 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.013 0.002 TYR O 39 PHE 0.011 0.003 PHE O 94 HIS 0.007 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00677 ( 7770) covalent geometry : angle 0.60953 (10470) hydrogen bonds : bond 0.02389 ( 456) hydrogen bonds : angle 4.37883 ( 1368) *********************** 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 211 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 175 time to evaluate : 0.305 Fit side-chains REVERT: A 46 GLU cc_start: 0.8447 (tt0) cc_final: 0.7978 (tm-30) REVERT: B 33 THR cc_start: 0.7308 (t) cc_final: 0.7087 (t) REVERT: B 46 GLU cc_start: 0.8489 (tt0) cc_final: 0.7913 (tm-30) REVERT: C 20 GLU cc_start: 0.8270 (mp0) cc_final: 0.7963 (mp0) REVERT: C 46 GLU cc_start: 0.8453 (tt0) cc_final: 0.8139 (tm-30) REVERT: D 33 THR cc_start: 0.7178 (OUTLIER) cc_final: 0.6764 (t) REVERT: D 65 ASN cc_start: 0.9191 (t0) cc_final: 0.8880 (t0) REVERT: F 46 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: G 35 GLU cc_start: 0.8272 (tm-30) cc_final: 0.7283 (tm-30) REVERT: H 35 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7345 (tm-30) REVERT: I 33 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6749 (t) REVERT: I 35 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7249 (tm-30) REVERT: J 35 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7303 (tm-30) REVERT: K 46 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: M 33 THR cc_start: 0.7111 (OUTLIER) cc_final: 0.6816 (t) REVERT: M 34 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8116 (mttt) REVERT: O 33 THR cc_start: 0.7163 (OUTLIER) cc_final: 0.6728 (t) REVERT: P 42 SER cc_start: 0.8880 (t) cc_final: 0.8554 (m) outliers start: 36 outliers final: 22 residues processed: 192 average time/residue: 0.6400 time to fit residues: 128.4319 Evaluate side-chains 202 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 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 46 GLU 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 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 17 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 24 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3643 r_free = 0.3643 target = 0.108714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089949 restraints weight = 9346.253| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.22 r_work: 0.3281 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 7770 Z= 0.304 Angle : 0.599 9.622 10470 Z= 0.328 Chirality : 0.055 0.140 1380 Planarity : 0.002 0.011 1290 Dihedral : 4.969 13.794 1110 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 4.49 % Allowed : 20.77 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.016 0.002 TYR I 39 PHE 0.011 0.003 PHE O 94 HIS 0.006 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00626 ( 7770) covalent geometry : angle 0.59922 (10470) hydrogen bonds : bond 0.02300 ( 456) hydrogen bonds : angle 4.37003 ( 1368) *********************** 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 : 0.326 Fit side-chains REVERT: A 46 GLU cc_start: 0.8467 (tt0) cc_final: 0.8040 (tm-30) REVERT: B 33 THR cc_start: 0.7468 (t) cc_final: 0.7231 (t) REVERT: B 46 GLU cc_start: 0.8502 (tt0) cc_final: 0.7948 (tm-30) REVERT: C 20 GLU cc_start: 0.8308 (mp0) cc_final: 0.8041 (mp0) REVERT: C 46 GLU cc_start: 0.8467 (tt0) cc_final: 0.8184 (tm-30) REVERT: D 33 THR cc_start: 0.7263 (OUTLIER) cc_final: 0.6856 (t) REVERT: D 65 ASN cc_start: 0.9156 (t0) cc_final: 0.8839 (t0) REVERT: F 24 GLN cc_start: 0.6658 (OUTLIER) cc_final: 0.5961 (mp10) REVERT: F 46 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: F 61 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5623 (mm-30) REVERT: G 35 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7323 (tm-30) REVERT: H 35 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7388 (tm-30) REVERT: I 33 THR cc_start: 0.7047 (OUTLIER) cc_final: 0.6821 (t) REVERT: I 35 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7265 (tm-30) REVERT: J 35 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7343 (tm-30) REVERT: K 46 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: L 58 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8786 (mttt) REVERT: M 33 THR cc_start: 0.7157 (OUTLIER) cc_final: 0.6846 (t) REVERT: M 34 LYS cc_start: 0.8363 (mtpt) cc_final: 0.8153 (mttt) REVERT: O 33 THR cc_start: 0.7214 (OUTLIER) cc_final: 0.6803 (t) REVERT: P 42 SER cc_start: 0.8863 (t) cc_final: 0.8571 (m) outliers start: 35 outliers final: 22 residues processed: 194 average time/residue: 0.6198 time to fit residues: 125.6430 Evaluate side-chains 205 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.207 ------------------------------------------------------------------------------- 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 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 24 GLN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 61 GLU 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 M residue 33 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 95 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 chunk 10 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 0.0010 chunk 53 optimal weight: 6.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.109516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090857 restraints weight = 9281.187| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.21 r_work: 0.3306 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 7770 Z= 0.243 Angle : 0.571 9.383 10470 Z= 0.312 Chirality : 0.054 0.122 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.824 13.518 1110 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.36 % Allowed : 20.90 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 TYR 0.013 0.002 TYR O 39 PHE 0.010 0.002 PHE O 94 HIS 0.005 0.003 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 7770) covalent geometry : angle 0.57108 (10470) hydrogen bonds : bond 0.02053 ( 456) hydrogen bonds : angle 4.28181 ( 1368) ********************** 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 199 residues out of total 780 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.282 Fit side-chains REVERT: A 46 GLU cc_start: 0.8440 (tt0) cc_final: 0.8025 (tm-30) REVERT: A 61 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5848 (mm-30) REVERT: B 33 THR cc_start: 0.7424 (t) cc_final: 0.7180 (t) REVERT: B 46 GLU cc_start: 0.8493 (tt0) cc_final: 0.7945 (tm-30) REVERT: C 20 GLU cc_start: 0.8294 (mp0) cc_final: 0.7990 (mp0) REVERT: C 46 GLU cc_start: 0.8444 (tt0) cc_final: 0.8162 (tm-30) REVERT: D 33 THR cc_start: 0.7238 (OUTLIER) cc_final: 0.6879 (t) REVERT: D 65 ASN cc_start: 0.9150 (t0) cc_final: 0.8827 (t0) REVERT: F 24 GLN cc_start: 0.6751 (OUTLIER) cc_final: 0.6085 (mp10) REVERT: F 46 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: F 61 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5657 (mm-30) REVERT: G 35 GLU cc_start: 0.8307 (tm-30) cc_final: 0.7304 (tm-30) REVERT: H 35 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7366 (tm-30) REVERT: I 33 THR cc_start: 0.7016 (OUTLIER) cc_final: 0.6784 (t) REVERT: I 35 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7240 (tm-30) REVERT: J 35 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7341 (tm-30) REVERT: K 46 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8121 (tt0) REVERT: K 61 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5502 (mm-30) REVERT: L 58 LYS cc_start: 0.9141 (OUTLIER) cc_final: 0.8740 (mttt) REVERT: M 33 THR cc_start: 0.7148 (OUTLIER) cc_final: 0.6828 (t) REVERT: M 34 LYS cc_start: 0.8392 (mtpt) cc_final: 0.8157 (mtpt) REVERT: O 33 THR cc_start: 0.7208 (OUTLIER) cc_final: 0.6791 (t) REVERT: P 42 SER cc_start: 0.8848 (t) cc_final: 0.8559 (m) outliers start: 34 outliers final: 21 residues processed: 182 average time/residue: 0.6103 time to fit residues: 116.1852 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 : 0.299 ------------------------------------------------------------------------------- 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 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 24 GLN Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 61 GLU 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 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 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 50 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 90 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 72 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 63 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3612 r_free = 0.3612 target = 0.106708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.087929 restraints weight = 9444.048| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.20 r_work: 0.3255 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.033 7770 Z= 0.390 Angle : 0.673 9.960 10470 Z= 0.370 Chirality : 0.057 0.164 1380 Planarity : 0.003 0.017 1290 Dihedral : 5.168 14.006 1110 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.00 % Allowed : 20.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.70 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR O 39 PHE 0.013 0.003 PHE O 94 HIS 0.008 0.004 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00807 ( 7770) covalent geometry : angle 0.67288 (10470) hydrogen bonds : bond 0.02623 ( 456) hydrogen bonds : angle 4.52703 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.87 seconds wall clock time: 50 minutes 39.93 seconds (3039.93 seconds total)