Starting phenix.real_space_refine on Tue Sep 24 08:50:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/09_2024/8a4l_15148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/09_2024/8a4l_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/09_2024/8a4l_15148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/09_2024/8a4l_15148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/09_2024/8a4l_15148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a4l_15148/09_2024/8a4l_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-5461/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: 2.43, per 1000 atoms: 0.31 Number of scatterers: 7755 At special positions: 0 Unit cell: (145.95, 141.75, 43.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1560 8.00 N 1350 7.00 C 4845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.1 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: 1.30 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: 2.32 Time building geometry restraints manager: 2.17 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' 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: 1.180 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.900 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.776 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: 1.5713 time to fit residues: 291.2466 Evaluate side-chains 141 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 0.890 Fit side-chains REVERT: B 46 GLU cc_start: 0.7627 (tt0) cc_final: 0.7418 (tm-30) REVERT: C 20 GLU cc_start: 0.7756 (mp0) cc_final: 0.7473 (mp0) REVERT: D 35 GLU cc_start: 0.7768 (tm-30) cc_final: 0.6987 (tm-30) REVERT: D 45 LYS cc_start: 0.8683 (tttm) cc_final: 0.8451 (tttm) REVERT: E 35 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7456 (tm-30) REVERT: H 35 GLU cc_start: 0.7834 (tm-30) cc_final: 0.6900 (tm-30) REVERT: I 35 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7130 (tm-30) REVERT: L 58 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8865 (mttt) REVERT: M 42 SER cc_start: 0.8539 (t) cc_final: 0.8322 (t) REVERT: O 35 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7027 (tm-30) REVERT: P 42 SER cc_start: 0.8528 (t) cc_final: 0.8266 (m) outliers start: 16 outliers final: 6 residues processed: 196 average time/residue: 1.5504 time to fit residues: 316.6886 Evaluate side-chains 191 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 52 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 G 65 ASN L 65 ASN O 65 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7770 Z= 0.176 Angle : 0.482 6.076 10470 Z= 0.262 Chirality : 0.052 0.123 1380 Planarity : 0.002 0.007 1290 Dihedral : 4.730 21.423 1110 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.95 % Allowed : 17.69 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.007 0.002 PHE G 94 TYR 0.007 0.001 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 196 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 173 time to evaluate : 0.868 Fit side-chains REVERT: C 20 GLU cc_start: 0.7782 (mp0) cc_final: 0.7549 (mp0) REVERT: D 35 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7029 (tm-30) REVERT: D 45 LYS cc_start: 0.8644 (tttm) cc_final: 0.8418 (tttm) REVERT: E 35 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7464 (tm-30) REVERT: E 45 LYS cc_start: 0.8484 (tttm) cc_final: 0.8198 (tttm) REVERT: H 35 GLU cc_start: 0.7769 (tm-30) cc_final: 0.6873 (tm-30) REVERT: I 35 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7046 (tm-30) REVERT: I 46 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7519 (tt0) REVERT: J 35 GLU cc_start: 0.7800 (tm-30) cc_final: 0.6980 (tm-30) REVERT: K 72 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8625 (m) REVERT: L 58 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8655 (mttt) REVERT: P 42 SER cc_start: 0.8447 (t) cc_final: 0.8194 (m) outliers start: 23 outliers final: 8 residues processed: 187 average time/residue: 1.5481 time to fit residues: 302.0197 Evaluate side-chains 173 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 162 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 I 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 72 THR Chi-restraints excluded: chain L residue 58 LYS 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 94 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 27 optimal weight: 9.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 7770 Z= 0.613 Angle : 0.687 9.085 10470 Z= 0.378 Chirality : 0.058 0.181 1380 Planarity : 0.003 0.008 1290 Dihedral : 5.430 24.529 1110 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.77 % Allowed : 18.59 % Favored : 75.64 % 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 0.009 0.004 HIS J 50 PHE 0.014 0.003 PHE M 94 TYR 0.007 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 194 time to evaluate : 0.869 Fit side-chains REVERT: B 34 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.7681 (mtpt) REVERT: B 46 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7278 (tm-30) REVERT: C 46 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: D 33 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7204 (t) REVERT: G 35 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7054 (tm-30) REVERT: H 35 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7124 (tm-30) REVERT: I 33 THR cc_start: 0.7343 (t) cc_final: 0.7118 (t) REVERT: I 35 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7057 (tm-30) REVERT: J 24 GLN cc_start: 0.6390 (mp10) cc_final: 0.5396 (mp10) REVERT: J 35 GLU cc_start: 0.7874 (tm-30) cc_final: 0.6994 (tm-30) REVERT: K 46 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: L 42 SER cc_start: 0.8361 (t) cc_final: 0.8089 (p) REVERT: O 33 THR cc_start: 0.7510 (t) cc_final: 0.7224 (t) REVERT: P 42 SER cc_start: 0.8509 (t) cc_final: 0.8255 (m) outliers start: 45 outliers final: 20 residues processed: 218 average time/residue: 1.4360 time to fit residues: 327.6791 Evaluate side-chains 212 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain B residue 34 LYS Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 46 GLU 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 64 THR Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 24 GLN Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 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 84 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7770 Z= 0.300 Angle : 0.536 8.405 10470 Z= 0.292 Chirality : 0.053 0.123 1380 Planarity : 0.002 0.008 1290 Dihedral : 4.833 18.438 1110 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.36 % Allowed : 20.26 % Favored : 75.38 % 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 0.004 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 198 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 164 time to evaluate : 0.802 Fit side-chains REVERT: B 46 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: C 46 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6754 (tm-30) REVERT: D 33 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7230 (t) REVERT: G 20 GLU cc_start: 0.7737 (mp0) cc_final: 0.7518 (mp0) REVERT: H 35 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7043 (tm-30) REVERT: I 33 THR cc_start: 0.7270 (OUTLIER) cc_final: 0.7007 (t) REVERT: I 35 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7078 (tm-30) REVERT: J 24 GLN cc_start: 0.6539 (mp10) cc_final: 0.6309 (mp10) REVERT: J 35 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7060 (tm-30) REVERT: K 46 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: L 58 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8789 (mttt) REVERT: M 33 THR cc_start: 0.7569 (OUTLIER) cc_final: 0.7307 (t) REVERT: O 33 THR cc_start: 0.7439 (t) cc_final: 0.7000 (t) REVERT: P 42 SER cc_start: 0.8452 (t) cc_final: 0.8199 (m) outliers start: 34 outliers final: 18 residues processed: 183 average time/residue: 1.4430 time to fit residues: 276.2320 Evaluate side-chains 185 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 46 GLU 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 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 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 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 34 optimal weight: 9.9990 chunk 91 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 7770 Z= 0.607 Angle : 0.683 10.485 10470 Z= 0.377 Chirality : 0.058 0.177 1380 Planarity : 0.003 0.008 1290 Dihedral : 5.332 21.095 1110 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 6.15 % Allowed : 18.33 % 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: -3.69 (0.19), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS J 50 PHE 0.015 0.004 PHE G 94 TYR 0.011 0.002 TYR O 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 238 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 190 time to evaluate : 0.900 Fit side-chains REVERT: B 46 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7300 (tm-30) REVERT: C 46 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7109 (tm-30) REVERT: D 33 THR cc_start: 0.7617 (OUTLIER) cc_final: 0.7205 (t) REVERT: G 35 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7016 (tm-30) REVERT: H 35 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7148 (tm-30) REVERT: I 33 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7100 (t) REVERT: I 35 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7106 (tm-30) REVERT: J 35 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7074 (tm-30) REVERT: K 46 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7487 (tt0) REVERT: L 42 SER cc_start: 0.8360 (t) cc_final: 0.8078 (p) REVERT: M 33 THR cc_start: 0.7553 (OUTLIER) cc_final: 0.7291 (t) REVERT: O 33 THR cc_start: 0.7609 (OUTLIER) cc_final: 0.7231 (t) REVERT: P 42 SER cc_start: 0.8526 (t) cc_final: 0.8271 (m) outliers start: 48 outliers final: 25 residues processed: 213 average time/residue: 1.4525 time to fit residues: 323.4280 Evaluate side-chains 217 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 46 GLU 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 64 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 46 GLU Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain O residue 87 SER 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 97 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7770 Z= 0.202 Angle : 0.507 8.709 10470 Z= 0.276 Chirality : 0.053 0.122 1380 Planarity : 0.002 0.007 1290 Dihedral : 4.555 13.119 1110 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.36 % Allowed : 21.28 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.20), residues: 1065 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.15), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.009 0.002 PHE G 94 TYR 0.008 0.002 TYR L 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 192 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 158 time to evaluate : 0.866 Fit side-chains REVERT: A 46 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7039 (tm-30) REVERT: A 72 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (m) REVERT: B 46 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6855 (tm-30) REVERT: C 46 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6767 (tm-30) REVERT: D 33 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7116 (t) REVERT: F 61 GLU cc_start: 0.5874 (OUTLIER) cc_final: 0.5405 (mm-30) REVERT: G 20 GLU cc_start: 0.7668 (mp0) cc_final: 0.7465 (mp0) REVERT: H 35 GLU cc_start: 0.7761 (tm-30) cc_final: 0.7069 (tm-30) REVERT: I 33 THR cc_start: 0.7076 (OUTLIER) cc_final: 0.6779 (t) REVERT: I 35 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7124 (tm-30) REVERT: J 35 GLU cc_start: 0.7872 (tm-30) cc_final: 0.7088 (tm-30) REVERT: L 58 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8651 (mttt) REVERT: M 33 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7137 (t) REVERT: O 33 THR cc_start: 0.7450 (OUTLIER) cc_final: 0.7030 (t) REVERT: P 42 SER cc_start: 0.8441 (t) cc_final: 0.8207 (m) outliers start: 34 outliers final: 15 residues processed: 177 average time/residue: 1.4331 time to fit residues: 265.6837 Evaluate side-chains 180 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 155 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 46 GLU 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 9 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 7770 Z= 0.428 Angle : 0.603 9.666 10470 Z= 0.330 Chirality : 0.055 0.143 1380 Planarity : 0.002 0.012 1290 Dihedral : 4.940 14.174 1110 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.74 % Allowed : 21.03 % Favored : 74.23 % 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 0.013 0.002 TYR O 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 209 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 0.888 Fit side-chains REVERT: A 61 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5498 (mm-30) REVERT: B 46 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7252 (tm-30) REVERT: C 46 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: D 33 THR cc_start: 0.7622 (OUTLIER) cc_final: 0.7135 (t) REVERT: F 61 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5377 (mm-30) REVERT: G 35 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7046 (tm-30) REVERT: H 35 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7131 (tm-30) REVERT: I 33 THR cc_start: 0.7298 (OUTLIER) cc_final: 0.7051 (t) REVERT: I 35 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7037 (tm-30) REVERT: J 35 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7099 (tm-30) REVERT: K 46 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: L 58 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8780 (mttt) REVERT: M 33 THR cc_start: 0.7543 (OUTLIER) cc_final: 0.7291 (t) REVERT: M 34 LYS cc_start: 0.8331 (mtpt) cc_final: 0.8082 (mttt) REVERT: O 33 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.7089 (t) REVERT: P 42 SER cc_start: 0.8505 (t) cc_final: 0.8255 (m) outliers start: 37 outliers final: 23 residues processed: 189 average time/residue: 1.4304 time to fit residues: 282.9813 Evaluate side-chains 203 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 46 GLU 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 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 45 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 56 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 7770 Z= 0.382 Angle : 0.591 9.238 10470 Z= 0.323 Chirality : 0.054 0.132 1380 Planarity : 0.002 0.010 1290 Dihedral : 4.906 14.020 1110 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.87 % Allowed : 21.41 % Favored : 73.72 % 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: -3.66 (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 O 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 205 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 167 time to evaluate : 0.834 Fit side-chains REVERT: A 61 GLU cc_start: 0.5981 (OUTLIER) cc_final: 0.5547 (mm-30) REVERT: B 46 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: C 46 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: D 33 THR cc_start: 0.7636 (OUTLIER) cc_final: 0.7297 (t) REVERT: F 61 GLU cc_start: 0.5973 (OUTLIER) cc_final: 0.5434 (mm-30) REVERT: G 35 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7038 (tm-30) REVERT: H 35 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7091 (tm-30) REVERT: I 33 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.7045 (t) REVERT: I 35 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7036 (tm-30) REVERT: J 35 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7082 (tm-30) REVERT: K 46 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7461 (tt0) REVERT: L 58 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8728 (mttt) REVERT: M 33 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7148 (t) REVERT: M 34 LYS cc_start: 0.8325 (mtpt) cc_final: 0.8053 (mttt) REVERT: O 33 THR cc_start: 0.7507 (OUTLIER) cc_final: 0.7145 (t) REVERT: P 42 SER cc_start: 0.8483 (t) cc_final: 0.8239 (m) outliers start: 38 outliers final: 24 residues processed: 185 average time/residue: 1.4470 time to fit residues: 279.9701 Evaluate side-chains 200 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 46 GLU 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 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 45 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 7.9990 chunk 60 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.032 7770 Z= 0.481 Angle : 0.658 9.889 10470 Z= 0.359 Chirality : 0.056 0.153 1380 Planarity : 0.003 0.016 1290 Dihedral : 5.100 14.066 1110 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.87 % Allowed : 21.92 % Favored : 73.21 % 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 0.007 0.003 HIS J 50 PHE 0.013 0.003 PHE G 94 TYR 0.017 0.002 TYR I 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 180 time to evaluate : 1.002 Fit side-chains REVERT: A 61 GLU cc_start: 0.6036 (OUTLIER) cc_final: 0.5595 (mm-30) REVERT: B 46 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7249 (tm-30) REVERT: C 46 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7094 (tm-30) REVERT: F 61 GLU cc_start: 0.5984 (OUTLIER) cc_final: 0.5413 (mm-30) REVERT: G 35 GLU cc_start: 0.8007 (tm-30) cc_final: 0.7029 (tm-30) REVERT: H 35 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7133 (tm-30) REVERT: I 33 THR cc_start: 0.7320 (OUTLIER) cc_final: 0.7074 (t) REVERT: I 35 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7063 (tm-30) REVERT: J 35 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7071 (tm-30) REVERT: K 46 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: L 58 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8782 (mttt) REVERT: M 33 THR cc_start: 0.7439 (OUTLIER) cc_final: 0.7169 (t) REVERT: M 34 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8104 (mttt) REVERT: O 33 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7162 (t) REVERT: P 42 SER cc_start: 0.8510 (t) cc_final: 0.8267 (m) outliers start: 38 outliers final: 25 residues processed: 198 average time/residue: 1.4893 time to fit residues: 308.6379 Evaluate side-chains 213 residues out of total 780 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 46 GLU 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 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 45 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain L residue 33 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 LYS Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 33 THR Chi-restraints excluded: chain M residue 72 THR Chi-restraints excluded: chain O residue 33 THR Chi-restraints excluded: chain O residue 58 LYS Chi-restraints excluded: chain O residue 72 THR Chi-restraints excluded: chain P residue 33 THR Chi-restraints excluded: chain P residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 83 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 ASN I 65 ASN L 65 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.110008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.091272 restraints weight = 9232.449| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.21 r_work: 0.3311 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7770 Z= 0.300 Angle : 0.581 9.226 10470 Z= 0.316 Chirality : 0.053 0.121 1380 Planarity : 0.002 0.018 1290 Dihedral : 4.788 13.575 1110 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.62 % Allowed : 22.69 % Favored : 72.69 % 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 H 50 PHE 0.010 0.002 PHE G 94 TYR 0.016 0.002 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4303.17 seconds wall clock time: 76 minutes 10.16 seconds (4570.16 seconds total)