Starting phenix.real_space_refine on Wed Jun 11 02:29:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cod_45776/06_2025/9cod_45776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cod_45776/06_2025/9cod_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_45776/06_2025/9cod_45776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cod_45776/06_2025/9cod_45776.map" model { file = "/net/cci-nas-00/data/ceres_data/9cod_45776/06_2025/9cod_45776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cod_45776/06_2025/9cod_45776.cif" } resolution = 4.7 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= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N Time building chain proxies: 5.79, per 1000 atoms: 0.47 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.43 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: 2.75 Time building geometry restraints manager: 3.53 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' } 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: 9.810 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: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.140 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 (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: -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 HIS 0.009 0.006 HIS C 10 PHE 0.007 0.002 PHE F 7 TYR 0.026 0.003 TYR B 76 ARG 0.001 0.000 ARG A 25 Details of bonding type rmsd hydrogen bonds : bond 0.20624 ( 90) hydrogen bonds : angle 7.74721 ( 225) covalent geometry : bond 0.00372 (12705) covalent geometry : angle 1.08153 (17340) *********************** 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 : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1238 time to fit residues: 2.6319 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 : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.0060 chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 0.0980 chunk 45 optimal weight: 0.0030 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 136 optimal weight: 0.0010 overall best weight: 0.1412 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.064379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.056976 restraints weight = 7231.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.058202 restraints weight = 5022.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.059085 restraints weight = 3780.969| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12705 Z= 0.167 Angle : 0.850 6.260 17340 Z= 0.454 Chirality : 0.047 0.128 1950 Planarity : 0.004 0.022 2295 Dihedral : 6.181 21.942 1695 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 3.88 % Allowed : 21.36 % Favored : 74.76 % Rotamer: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % 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: -4.49 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.43 (0.32), residues: 255 loop : -3.45 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS N 10 PHE 0.006 0.001 PHE G 54 TYR 0.017 0.002 TYR I 76 ARG 0.001 0.000 ARG H 66 Details of bonding type rmsd hydrogen bonds : bond 0.01844 ( 90) hydrogen bonds : angle 4.90133 ( 225) covalent geometry : bond 0.00337 (12705) covalent geometry : angle 0.85013 (17340) *********************** 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 15 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.093 Fit side-chains REVERT: A 46 MET cc_start: 0.8042 (mmp) cc_final: 0.7731 (mmm) REVERT: A 76 TYR cc_start: 0.8718 (p90) cc_final: 0.8470 (p90) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1099 time to fit residues: 1.9039 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 125 optimal weight: 0.0040 chunk 78 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 0.0000 chunk 33 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 36 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.060177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.052977 restraints weight = 7609.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054111 restraints weight = 5450.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055029 restraints weight = 4114.567| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 12705 Z= 0.164 Angle : 0.844 7.347 17340 Z= 0.449 Chirality : 0.047 0.126 1950 Planarity : 0.004 0.016 2295 Dihedral : 5.981 22.474 1695 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 23.86 Ramachandran Plot: Outliers : 3.88 % Allowed : 25.24 % Favored : 70.87 % 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 (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: -4.58 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.44 (0.33), residues: 255 loop : -3.53 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS C 10 PHE 0.005 0.001 PHE J 22 TYR 0.011 0.002 TYR N 84 ARG 0.001 0.000 ARG D 25 Details of bonding type rmsd hydrogen bonds : bond 0.02024 ( 90) hydrogen bonds : angle 5.38009 ( 225) covalent geometry : bond 0.00368 (12705) covalent geometry : angle 0.84368 (17340) *********************** 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 13 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.090 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0804 time to fit residues: 1.2736 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 : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 0.0570 chunk 59 optimal weight: 0.0060 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 0.0370 chunk 133 optimal weight: 0.0010 chunk 105 optimal weight: 3.9990 chunk 3 optimal weight: 0.0770 chunk 31 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.0970 overall best weight: 0.0356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.063096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.055432 restraints weight = 7233.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.056611 restraints weight = 5091.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.057487 restraints weight = 3888.613| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12705 Z= 0.154 Angle : 0.804 6.505 17340 Z= 0.432 Chirality : 0.046 0.135 1950 Planarity : 0.003 0.015 2295 Dihedral : 5.938 21.950 1695 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 11.36 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 (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: -4.36 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.54 (0.43), residues: 180 loop : -3.47 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 36 PHE 0.007 0.002 PHE G 9 TYR 0.021 0.002 TYR N 76 ARG 0.000 0.000 ARG H 25 Details of bonding type rmsd hydrogen bonds : bond 0.01572 ( 90) hydrogen bonds : angle 4.87649 ( 225) covalent geometry : bond 0.00320 (12705) covalent geometry : angle 0.80359 (17340) *********************** 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 17 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.097 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.4839 (pm20) cc_final: 0.4465 (pm20) REVERT: A 76 TYR cc_start: 0.8673 (p90) cc_final: 0.8387 (p90) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0879 time to fit residues: 1.7992 Evaluate side-chains 15 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 0.0050 chunk 44 optimal weight: 0.4980 chunk 36 optimal weight: 0.0970 chunk 116 optimal weight: 0.0370 chunk 88 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 31 optimal weight: 0.0030 chunk 47 optimal weight: 4.9990 overall best weight: 0.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.060925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054242 restraints weight = 7164.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055369 restraints weight = 4991.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.056246 restraints weight = 3713.939| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2982 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= 0.160 Angle : 0.813 7.884 17340 Z= 0.439 Chirality : 0.044 0.131 1950 Planarity : 0.003 0.016 2295 Dihedral : 6.559 21.722 1695 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 3.88 % Allowed : 22.33 % Favored : 73.79 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.18), residues: 1545 helix: None (None), residues: 0 sheet: -1.57 (0.42), residues: 180 loop : -3.71 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 36 PHE 0.010 0.002 PHE A 22 TYR 0.016 0.002 TYR E 76 ARG 0.001 0.000 ARG M 25 Details of bonding type rmsd hydrogen bonds : bond 0.01806 ( 90) hydrogen bonds : angle 4.61543 ( 225) covalent geometry : bond 0.00324 (12705) covalent geometry : angle 0.81344 (17340) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.090 Fit side-chains REVERT: G 76 TYR cc_start: 0.8211 (p90) cc_final: 0.7993 (p90) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1013 time to fit residues: 1.8750 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 : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 139 optimal weight: 1.9990 chunk 53 optimal weight: 0.0370 chunk 88 optimal weight: 0.8980 chunk 122 optimal weight: 0.0170 chunk 13 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 71 optimal weight: 0.4980 chunk 135 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.059843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053212 restraints weight = 6924.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.054345 restraints weight = 4879.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.054965 restraints weight = 3631.129| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12705 Z= 0.146 Angle : 0.827 7.273 17340 Z= 0.438 Chirality : 0.045 0.137 1950 Planarity : 0.003 0.016 2295 Dihedral : 6.355 21.676 1695 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 3.88 % Allowed : 22.33 % Favored : 73.79 % 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 (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: -4.58 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.60 (0.43), residues: 180 loop : -3.65 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS K 36 PHE 0.007 0.001 PHE O 22 TYR 0.013 0.002 TYR A 76 ARG 0.000 0.000 ARG D 66 Details of bonding type rmsd hydrogen bonds : bond 0.01556 ( 90) hydrogen bonds : angle 4.67048 ( 225) covalent geometry : bond 0.00308 (12705) covalent geometry : angle 0.82695 (17340) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 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 : 0.088 Fit side-chains REVERT: G 76 TYR cc_start: 0.8259 (p90) cc_final: 0.8039 (p90) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0720 time to fit residues: 1.0866 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 : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 119 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 146 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.0370 chunk 86 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.052835 restraints weight = 7229.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053958 restraints weight = 4961.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.054762 restraints weight = 3699.688| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3516 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= 0.147 Angle : 0.824 6.995 17340 Z= 0.437 Chirality : 0.045 0.130 1950 Planarity : 0.003 0.017 2295 Dihedral : 6.165 21.763 1695 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 16.81 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 (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: -4.75 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.25 (0.32), residues: 255 loop : -3.73 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS K 36 PHE 0.010 0.001 PHE B 22 TYR 0.010 0.001 TYR L 76 ARG 0.001 0.000 ARG I 66 Details of bonding type rmsd hydrogen bonds : bond 0.01507 ( 90) hydrogen bonds : angle 4.82096 ( 225) covalent geometry : bond 0.00315 (12705) covalent geometry : angle 0.82423 (17340) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2884 Ramachandran restraints generated. 1442 Oldfield, 0 Emsley, 1442 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.102 Fit side-chains REVERT: A 59 GLU cc_start: 0.7304 (mp0) cc_final: 0.6777 (mp0) REVERT: A 76 TYR cc_start: 0.8720 (p90) cc_final: 0.8425 (p90) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0789 time to fit residues: 1.4461 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 : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 148 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 116 optimal weight: 0.0000 chunk 21 optimal weight: 0.9980 chunk 71 optimal weight: 0.0060 chunk 128 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 79 optimal weight: 0.0170 chunk 119 optimal weight: 0.6980 chunk 102 optimal weight: 0.0030 overall best weight: 0.1248 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.062354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.054548 restraints weight = 6888.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.055700 restraints weight = 4967.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.056504 restraints weight = 3824.655| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12705 Z= 0.156 Angle : 0.894 11.436 17340 Z= 0.474 Chirality : 0.044 0.133 1950 Planarity : 0.004 0.023 2295 Dihedral : 6.168 21.235 1695 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 3.88 % Allowed : 20.39 % Favored : 75.73 % 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: -4.52 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.89 (0.41), residues: 180 loop : -3.55 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS K 36 PHE 0.006 0.001 PHE G 7 TYR 0.012 0.001 TYR L 76 ARG 0.000 0.000 ARG O 66 Details of bonding type rmsd hydrogen bonds : bond 0.01558 ( 90) hydrogen bonds : angle 4.69876 ( 225) covalent geometry : bond 0.00329 (12705) covalent geometry : angle 0.89437 (17340) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.101 Fit side-chains REVERT: C 90 VAL cc_start: 0.8915 (t) cc_final: 0.8211 (t) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0731 time to fit residues: 1.3753 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 73 optimal weight: 0.0570 chunk 130 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 145 optimal weight: 0.0270 chunk 144 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 54 optimal weight: 2.9990 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.061527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.053656 restraints weight = 7104.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054859 restraints weight = 4999.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055725 restraints weight = 3793.308| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4229 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= 0.152 Angle : 0.890 10.701 17340 Z= 0.469 Chirality : 0.046 0.132 1950 Planarity : 0.004 0.019 2295 Dihedral : 6.175 20.920 1695 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 4.85 % Allowed : 19.42 % Favored : 75.73 % 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: -4.51 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.08 (0.40), residues: 180 loop : -3.52 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS K 36 PHE 0.004 0.001 PHE M 7 TYR 0.007 0.001 TYR O 84 ARG 0.000 0.000 ARG B 28 Details of bonding type rmsd hydrogen bonds : bond 0.01611 ( 90) hydrogen bonds : angle 4.43402 ( 225) covalent geometry : bond 0.00316 (12705) covalent geometry : angle 0.89033 (17340) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 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 : 0.099 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0686 time to fit residues: 1.2125 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 : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 131 optimal weight: 0.0030 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 0.3980 chunk 29 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 1 optimal weight: 0.0270 chunk 136 optimal weight: 0.0170 chunk 92 optimal weight: 0.3980 overall best weight: 0.1686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.063091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.054988 restraints weight = 7814.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056121 restraints weight = 5656.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.056967 restraints weight = 4378.697| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.4422 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= 0.147 Angle : 0.866 10.456 17340 Z= 0.456 Chirality : 0.046 0.139 1950 Planarity : 0.004 0.018 2295 Dihedral : 5.944 19.255 1695 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 4.85 % Allowed : 18.45 % Favored : 76.70 % 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 (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: -4.86 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -3.08 (0.25), residues: 375 loop : -3.57 (0.16), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 10 PHE 0.005 0.001 PHE M 54 TYR 0.025 0.002 TYR H 76 ARG 0.000 0.000 ARG M 28 Details of bonding type rmsd hydrogen bonds : bond 0.01643 ( 90) hydrogen bonds : angle 4.46794 ( 225) covalent geometry : bond 0.00313 (12705) covalent geometry : angle 0.86614 (17340) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2678 Ramachandran restraints generated. 1339 Oldfield, 0 Emsley, 1339 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 : 0.089 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0653 time to fit residues: 1.0838 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 : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 147 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 54 optimal weight: 0.0670 chunk 138 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 142 optimal weight: 0.0370 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.061378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.053888 restraints weight = 7378.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054982 restraints weight = 5213.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.055840 restraints weight = 3916.062| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4722 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= 0.145 Angle : 0.860 10.162 17340 Z= 0.451 Chirality : 0.044 0.128 1950 Planarity : 0.003 0.018 2295 Dihedral : 5.675 20.283 1695 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 4.85 % Allowed : 20.39 % Favored : 74.76 % 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 (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: -4.35 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.44 (0.48), residues: 150 loop : -3.45 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS N 10 PHE 0.008 0.001 PHE M 22 TYR 0.008 0.001 TYR F 84 ARG 0.001 0.000 ARG I 25 Details of bonding type rmsd hydrogen bonds : bond 0.01471 ( 90) hydrogen bonds : angle 4.55454 ( 225) covalent geometry : bond 0.00308 (12705) covalent geometry : angle 0.86035 (17340) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3688.02 seconds wall clock time: 67 minutes 1.46 seconds (4021.46 seconds total)