Starting phenix.real_space_refine on Fri Jul 3 05:21:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cod_45776/07_2026/9cod_45776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cod_45776/07_2026/9cod_45776.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cod_45776/07_2026/9cod_45776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cod_45776/07_2026/9cod_45776.map" model { file = "/net/cci-nas-00/data/ceres_data/9cod_45776/07_2026/9cod_45776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cod_45776/07_2026/9cod_45776.cif" } resolution = 4.7 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= 0.000 sd= 0.001 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: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 7800 2.51 5 N 1890 2.21 5 O 2625 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12405 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 1.37, per 1000 atoms: 0.11 Number of scatterers: 12405 At special positions: 0 Unit cell: (187.04, 185.92, 51.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2625 8.00 N 1890 7.00 C 7800 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: 0.81 Conformation dependent library (CDL) restraints added in 642.3 milliseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 30 sheets defined 0.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR A 44 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 24 " --> pdb=" O TYR A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY A 30 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 38 " --> pdb=" O GLY A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR B 44 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 24 " --> pdb=" O TYR B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY B 30 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 38 " --> pdb=" O GLY B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR C 44 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 24 " --> pdb=" O TYR C 44 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY C 30 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 38 " --> pdb=" O GLY C 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR D 44 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 24 " --> pdb=" O TYR D 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY D 30 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 38 " --> pdb=" O GLY D 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR E 44 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL E 24 " --> pdb=" O TYR E 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY E 30 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 38 " --> pdb=" O GLY E 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR F 44 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL F 24 " --> pdb=" O TYR F 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY F 30 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 38 " --> pdb=" O GLY F 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR G 44 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL G 24 " --> pdb=" O TYR G 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY G 30 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 38 " --> pdb=" O GLY G 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 43 through 44 removed outlier: 3.657A pdb=" N TYR H 44 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL H 24 " --> pdb=" O TYR H 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY H 30 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 38 " --> pdb=" O GLY H 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR I 44 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL I 24 " --> pdb=" O TYR I 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY I 30 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL I 38 " --> pdb=" O GLY I 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR J 44 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL J 24 " --> pdb=" O TYR J 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY J 30 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL J 38 " --> pdb=" O GLY J 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR K 44 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL K 24 " --> pdb=" O TYR K 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY K 30 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL K 38 " --> pdb=" O GLY K 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR L 44 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL L 24 " --> pdb=" O TYR L 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY L 30 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL L 38 " --> pdb=" O GLY L 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR M 44 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL M 24 " --> pdb=" O TYR M 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY M 30 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL M 38 " --> pdb=" O GLY M 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'N' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR N 44 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL N 24 " --> pdb=" O TYR N 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY N 30 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL N 38 " --> pdb=" O GLY N 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'O' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR O 44 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL O 24 " --> pdb=" O TYR O 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY O 30 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL O 38 " --> pdb=" O GLY O 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 90 hydrogen bonds defined for protein. 225 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: 1.50 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4080 1.35 - 1.47: 3118 1.47 - 1.59: 5357 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 12705 Sorted by residual: bond pdb=" CA HIS K 10 " pdb=" CB HIS K 10 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.27e-02 6.20e+03 2.36e+00 bond pdb=" CA HIS G 10 " pdb=" CB HIS G 10 " ideal model delta sigma weight residual 1.524 1.544 -0.019 1.27e-02 6.20e+03 2.36e+00 bond pdb=" CA HIS I 10 " pdb=" CB HIS I 10 " ideal model delta sigma weight residual 1.524 1.544 -0.019 1.27e-02 6.20e+03 2.28e+00 bond pdb=" CA HIS D 10 " pdb=" CB HIS D 10 " ideal model delta sigma weight residual 1.524 1.544 -0.019 1.27e-02 6.20e+03 2.28e+00 bond pdb=" CA HIS N 10 " pdb=" CB HIS N 10 " ideal model delta sigma weight residual 1.524 1.543 -0.019 1.27e-02 6.20e+03 2.24e+00 ... (remaining 12700 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 16566 2.35 - 4.70: 670 4.70 - 7.04: 59 7.04 - 9.39: 30 9.39 - 11.74: 15 Bond angle restraints: 17340 Sorted by residual: angle pdb=" C THR C 48 " pdb=" N ASP C 49 " pdb=" CA ASP C 49 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C THR M 48 " pdb=" N ASP M 49 " pdb=" CA ASP M 49 " ideal model delta sigma weight residual 121.54 133.28 -11.74 1.91e+00 2.74e-01 3.78e+01 angle pdb=" C THR F 48 " pdb=" N ASP F 49 " pdb=" CA ASP F 49 " ideal model delta sigma weight residual 121.54 133.27 -11.73 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C THR B 48 " pdb=" N ASP B 49 " pdb=" CA ASP B 49 " ideal model delta sigma weight residual 121.54 133.27 -11.73 1.91e+00 2.74e-01 3.77e+01 angle pdb=" C THR J 48 " pdb=" N ASP J 49 " pdb=" CA ASP J 49 " ideal model delta sigma weight residual 121.54 133.27 -11.73 1.91e+00 2.74e-01 3.77e+01 ... (remaining 17335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 6673 15.31 - 30.62: 722 30.62 - 45.93: 180 45.93 - 61.24: 30 61.24 - 76.55: 15 Dihedral angle restraints: 7620 sinusoidal: 2940 harmonic: 4680 Sorted by residual: dihedral pdb=" CA ALA G 34 " pdb=" C ALA G 34 " pdb=" N GLU G 35 " pdb=" CA GLU G 35 " ideal model delta harmonic sigma weight residual 180.00 -157.25 -22.75 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ALA C 34 " pdb=" C ALA C 34 " pdb=" N GLU C 35 " pdb=" CA GLU C 35 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ALA M 34 " pdb=" C ALA M 34 " pdb=" N GLU M 35 " pdb=" CA GLU M 35 " ideal model delta harmonic sigma weight residual -180.00 -157.28 -22.72 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 7617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1062 0.028 - 0.055: 497 0.055 - 0.083: 253 0.083 - 0.111: 111 0.111 - 0.139: 27 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CB VAL G 5 " pdb=" CA VAL G 5 " pdb=" CG1 VAL G 5 " pdb=" CG2 VAL G 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CB VAL F 5 " pdb=" CA VAL F 5 " pdb=" CG1 VAL F 5 " pdb=" CG2 VAL F 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CB VAL I 5 " pdb=" CA VAL I 5 " pdb=" CG1 VAL I 5 " pdb=" CG2 VAL I 5 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1947 not shown) Planarity restraints: 2295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 76 " -0.008 2.00e-02 2.50e+03 1.09e-02 2.36e+00 pdb=" CG TYR B 76 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 76 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 76 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR B 76 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 76 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 76 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 76 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 76 " -0.008 2.00e-02 2.50e+03 1.08e-02 2.34e+00 pdb=" CG TYR M 76 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR M 76 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR M 76 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR M 76 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR M 76 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR M 76 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 76 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR J 76 " -0.008 2.00e-02 2.50e+03 1.08e-02 2.34e+00 pdb=" CG TYR J 76 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR J 76 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR J 76 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR J 76 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR J 76 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR J 76 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR J 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 2292 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1038 2.72 - 3.27: 14023 3.27 - 3.81: 20636 3.81 - 4.36: 23440 4.36 - 4.90: 38815 Nonbonded interactions: 97952 Sorted by model distance: nonbonded pdb=" O GLU A 20 " pdb=" OG1 THR A 48 " model vdw 2.175 3.040 nonbonded pdb=" O GLU E 20 " pdb=" OG1 THR E 48 " model vdw 2.175 3.040 nonbonded pdb=" O GLU J 20 " pdb=" OG1 THR J 48 " model vdw 2.175 3.040 nonbonded pdb=" O GLU G 20 " pdb=" OG1 THR G 48 " model vdw 2.175 3.040 nonbonded pdb=" O GLU F 20 " pdb=" OG1 THR F 48 " model vdw 2.175 3.040 ... (remaining 97947 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 'N' selection = chain 'O' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.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 'N' selection = chain 'O' } Set refine NCS operators NCS operators will be refined. 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 group one per residue 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: 13.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 9.260 Find NCS groups from input model: 0.070 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 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 0.039 12705 Z= 0.209 Angle : 1.082 11.741 17340 Z= 0.614 Chirality : 0.044 0.139 1950 Planarity : 0.004 0.027 2295 Dihedral : 13.738 76.554 4590 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 3.88 % Allowed : 24.27 % Favored : 71.84 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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 are not related in a simple way. whole: -4.85 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -3.26 (0.25), residues: 375 loop : -3.50 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 25 TYR 0.026 0.003 TYR B 76 PHE 0.007 0.002 PHE F 7 HIS 0.009 0.006 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.21 (12705) covalent geometry : angle 1.08153 / 0.61 (17340) hydrogen bonds : bond 0.20624 / 12.96 ( 90) hydrogen bonds : angle 7.74721 / 5.22 ( 225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0460 time to fit residues: 0.9902 Evaluate side-chains 12 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 10 HIS A 19 ASN A 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.063851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.056895 restraints weight = 7424.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.057944 restraints weight = 5132.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.058700 restraints weight = 3878.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.059188 restraints weight = 3125.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.059667 restraints weight = 2649.302| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12705 Z= 0.167 Angle : 0.870 6.226 17340 Z= 0.462 Chirality : 0.049 0.154 1950 Planarity : 0.004 0.017 2295 Dihedral : 6.156 22.367 1695 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 3.88 % Allowed : 24.27 % Favored : 71.84 % Rotamer: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % 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 are not related in a simple way. whole: -4.82 (0.20), residues: 1545 helix: None (None), residues: 0 sheet: -3.39 (0.25), residues: 390 loop : -3.40 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 66 TYR 0.016 0.003 TYR I 76 PHE 0.003 0.001 PHE L 7 HIS 0.008 0.004 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (12705) covalent geometry : angle 0.87018 / 0.46 (17340) hydrogen bonds : bond 0.01481 / 0.97 ( 90) hydrogen bonds : angle 4.91974 / 3.30 ( 225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.033 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0407 time to fit residues: 0.6513 Evaluate side-chains 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 HIS C 19 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.056027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.050220 restraints weight = 7643.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.051102 restraints weight = 5035.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.051787 restraints weight = 3677.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.052303 restraints weight = 2832.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.052666 restraints weight = 2306.457| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 12705 Z= 0.230 Angle : 0.938 7.604 17340 Z= 0.502 Chirality : 0.051 0.167 1950 Planarity : 0.005 0.019 2295 Dihedral : 6.540 22.726 1695 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 3.88 % Allowed : 29.13 % Favored : 66.99 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.15 (0.18), residues: 1545 helix: None (None), residues: 0 sheet: -3.03 (0.28), residues: 330 loop : -3.90 (0.15), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG O 25 TYR 0.016 0.003 TYR E 84 PHE 0.009 0.002 PHE M 22 HIS 0.010 0.004 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.23 (12705) covalent geometry : angle 0.93783 / 0.50 (17340) hydrogen bonds : bond 0.01747 / 1.14 ( 90) hydrogen bonds : angle 6.02327 / 4.06 ( 225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0579 time to fit residues: 0.7340 Evaluate side-chains 9 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 21 optimal weight: 0.0010 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 0.0870 chunk 44 optimal weight: 3.9990 overall best weight: 0.5168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 10 HIS G 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.054109 restraints weight = 6755.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.055276 restraints weight = 4727.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.056001 restraints weight = 3603.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.056541 restraints weight = 2904.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.056829 restraints weight = 2428.456| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12705 Z= 0.155 Angle : 0.846 6.443 17340 Z= 0.448 Chirality : 0.048 0.139 1950 Planarity : 0.004 0.015 2295 Dihedral : 6.245 21.123 1695 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 3.88 % Allowed : 19.42 % Favored : 76.70 % Rotamer: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.73 (0.28), residues: 315 loop : -3.64 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG I 66 TYR 0.007 0.001 TYR H 44 PHE 0.008 0.001 PHE I 9 HIS 0.012 0.005 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (12705) covalent geometry : angle 0.84569 / 0.45 (17340) hydrogen bonds : bond 0.01126 / 0.75 ( 90) hydrogen bonds : angle 5.02173 / 3.39 ( 225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0290 time to fit residues: 0.4274 Evaluate side-chains 12 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 0.0000 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 103 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 149 optimal weight: 0.6980 chunk 145 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 1 optimal weight: 0.0010 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 10 HIS C 19 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.061253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.054451 restraints weight = 7661.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.055472 restraints weight = 5346.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.056192 restraints weight = 3988.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.056768 restraints weight = 3198.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.057155 restraints weight = 2677.450| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12705 Z= 0.152 Angle : 0.853 9.514 17340 Z= 0.451 Chirality : 0.047 0.144 1950 Planarity : 0.004 0.014 2295 Dihedral : 6.280 21.106 1695 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 3.88 % Allowed : 24.27 % Favored : 71.84 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 are not related in a simple way. whole: -4.73 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.35 (0.33), residues: 255 loop : -3.69 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 66 TYR 0.021 0.002 TYR F 76 PHE 0.004 0.001 PHE I 9 HIS 0.011 0.004 HIS C 10 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (12705) covalent geometry : angle 0.85286 / 0.45 (17340) hydrogen bonds : bond 0.01195 / 0.80 ( 90) hydrogen bonds : angle 4.90287 / 3.32 ( 225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0284 time to fit residues: 0.4309 Evaluate side-chains 12 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 0.0870 chunk 112 optimal weight: 0.0870 chunk 79 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.0270 chunk 123 optimal weight: 0.0870 chunk 95 optimal weight: 0.0070 chunk 56 optimal weight: 3.9990 chunk 22 optimal weight: 0.0040 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.0070 overall best weight: 0.0264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.062614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054934 restraints weight = 7416.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.056041 restraints weight = 5198.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.056848 restraints weight = 3952.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.057423 restraints weight = 3168.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.057844 restraints weight = 2675.859| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12705 Z= 0.161 Angle : 0.847 7.346 17340 Z= 0.449 Chirality : 0.045 0.142 1950 Planarity : 0.003 0.015 2295 Dihedral : 6.130 20.725 1695 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 3.88 % Allowed : 19.42 % Favored : 76.70 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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 are not related in a simple way. whole: -4.44 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.78 (0.42), residues: 180 loop : -3.50 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 25 TYR 0.005 0.001 TYR O 98 PHE 0.008 0.002 PHE H 88 HIS 0.005 0.002 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (12705) covalent geometry : angle 0.84743 / 0.45 (17340) hydrogen bonds : bond 0.01609 / 1.08 ( 90) hydrogen bonds : angle 4.62612 / 3.15 ( 225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0309 time to fit residues: 0.6719 Evaluate side-chains 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 121 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 128 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.059725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.052733 restraints weight = 7396.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.053809 restraints weight = 5148.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054532 restraints weight = 3855.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054533 restraints weight = 3113.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.054533 restraints weight = 3112.515| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12705 Z= 0.175 Angle : 0.914 9.723 17340 Z= 0.489 Chirality : 0.046 0.135 1950 Planarity : 0.004 0.023 2295 Dihedral : 6.800 23.641 1695 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 3.88 % Allowed : 20.39 % Favored : 75.73 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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 are not related in a simple way. whole: -4.60 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.80 (0.42), residues: 180 loop : -3.64 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 28 TYR 0.024 0.002 TYR I 76 PHE 0.007 0.001 PHE M 22 HIS 0.006 0.004 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (12705) covalent geometry : angle 0.91425 / 0.49 (17340) hydrogen bonds : bond 0.01460 / 0.95 ( 90) hydrogen bonds : angle 4.68715 / 3.18 ( 225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0292 time to fit residues: 0.4765 Evaluate side-chains 10 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.057130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.050082 restraints weight = 7897.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.051188 restraints weight = 5453.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.051944 restraints weight = 4087.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.052553 restraints weight = 3270.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052808 restraints weight = 2699.565| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 12705 Z= 0.175 Angle : 0.929 9.287 17340 Z= 0.492 Chirality : 0.047 0.135 1950 Planarity : 0.004 0.017 2295 Dihedral : 6.845 21.759 1695 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 3.88 % Allowed : 23.30 % Favored : 72.82 % 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 are not related in a simple way. whole: -4.90 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.49 (0.31), residues: 255 loop : -3.81 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 25 TYR 0.011 0.002 TYR G 84 PHE 0.006 0.001 PHE O 9 HIS 0.004 0.002 HIS K 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.17 (12705) covalent geometry : angle 0.92884 / 0.49 (17340) hydrogen bonds : bond 0.01394 / 0.93 ( 90) hydrogen bonds : angle 5.21258 / 3.52 ( 225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.022 Fit side-chains REVERT: A 59 GLU cc_start: 0.7798 (mp0) cc_final: 0.7487 (mp0) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0253 time to fit residues: 0.3419 Evaluate side-chains 10 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 47 optimal weight: 0.0470 chunk 101 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.057480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.050080 restraints weight = 7723.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.051151 restraints weight = 5471.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.051929 restraints weight = 4166.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052502 restraints weight = 3330.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.052731 restraints weight = 2783.478| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.4224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12705 Z= 0.150 Angle : 0.892 8.945 17340 Z= 0.470 Chirality : 0.046 0.138 1950 Planarity : 0.004 0.018 2295 Dihedral : 6.619 20.635 1695 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 4.85 % Allowed : 20.39 % Favored : 74.76 % 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 are not related in a simple way. whole: -4.98 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -3.17 (0.26), residues: 390 loop : -3.66 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 25 TYR 0.026 0.002 TYR H 76 PHE 0.005 0.001 PHE O 9 HIS 0.004 0.002 HIS H 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (12705) covalent geometry : angle 0.89206 / 0.47 (17340) hydrogen bonds : bond 0.01046 / 0.70 ( 90) hydrogen bonds : angle 4.85398 / 3.29 ( 225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.036 Fit side-chains REVERT: A 59 GLU cc_start: 0.7704 (mp0) cc_final: 0.7343 (mp0) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0323 time to fit residues: 0.4490 Evaluate side-chains 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 76 optimal weight: 0.2980 chunk 124 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.4980 chunk 22 optimal weight: 0.0070 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 0.0870 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.059285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052510 restraints weight = 6979.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053607 restraints weight = 4856.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054356 restraints weight = 3618.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054971 restraints weight = 2890.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055436 restraints weight = 2376.771| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12705 Z= 0.148 Angle : 0.890 9.063 17340 Z= 0.468 Chirality : 0.045 0.140 1950 Planarity : 0.004 0.018 2295 Dihedral : 6.405 20.761 1695 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 4.85 % Allowed : 22.33 % Favored : 72.82 % 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 are not related in a simple way. whole: -4.82 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -3.37 (0.24), residues: 405 loop : -3.40 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG M 66 TYR 0.025 0.002 TYR H 76 PHE 0.006 0.001 PHE M 88 HIS 0.004 0.002 HIS H 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (12705) covalent geometry : angle 0.89047 / 0.47 (17340) hydrogen bonds : bond 0.01189 / 0.78 ( 90) hydrogen bonds : angle 4.90532 / 3.34 ( 225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.032 Fit side-chains REVERT: A 59 GLU cc_start: 0.7483 (mp0) cc_final: 0.7130 (mp0) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0259 time to fit residues: 0.4441 Evaluate side-chains 10 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 118 optimal weight: 0.3980 chunk 44 optimal weight: 0.4980 chunk 149 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 0.0270 chunk 138 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.058592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.051582 restraints weight = 7372.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.052691 restraints weight = 5139.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.053463 restraints weight = 3868.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054028 restraints weight = 3075.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054565 restraints weight = 2573.206| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12705 Z= 0.145 Angle : 0.857 8.808 17340 Z= 0.450 Chirality : 0.045 0.138 1950 Planarity : 0.003 0.017 2295 Dihedral : 6.114 20.876 1695 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 4.85 % Allowed : 20.39 % Favored : 74.76 % 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 are not related in a simple way. whole: -4.81 (0.20), residues: 1545 helix: None (None), residues: 0 sheet: -3.36 (0.23), residues: 435 loop : -3.35 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG I 66 TYR 0.026 0.002 TYR H 76 PHE 0.009 0.001 PHE F 22 HIS 0.004 0.002 HIS H 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (12705) covalent geometry : angle 0.85723 / 0.45 (17340) hydrogen bonds : bond 0.01368 / 0.93 ( 90) hydrogen bonds : angle 5.00624 / 3.40 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.98 seconds wall clock time: 22 minutes 51.26 seconds (1371.26 seconds total)