Starting phenix.real_space_refine on Sat Nov 16 23:43:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cod_45776/11_2024/9cod_45776.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cod_45776/11_2024/9cod_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cod_45776/11_2024/9cod_45776.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cod_45776/11_2024/9cod_45776.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cod_45776/11_2024/9cod_45776.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9cod_45776/11_2024/9cod_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-5513/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: 6.00, per 1000 atoms: 0.48 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: 2.82 Conformation dependent library (CDL) restraints added in 1.7 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: 1.28 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: 2.82 Time building geometry restraints manager: 3.32 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain '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: 6.140 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 26.910 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.080 ------------------------------------------------------------------------------- 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= 0.249 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 *********************** 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 : 0.107 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1234 time to fit residues: 2.6400 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 : 0.111 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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= 0.228 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 *********************** 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 : 0.091 Fit side-chains REVERT: A 46 MET cc_start: 0.8208 (mmp) cc_final: 0.7904 (mmm) REVERT: A 76 TYR cc_start: 0.8728 (p90) cc_final: 0.8501 (p90) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1161 time to fit residues: 2.0063 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 : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 chunk 113 optimal weight: 0.8980 chunk 92 optimal weight: 0.0570 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 0.0170 chunk 135 optimal weight: 2.9990 chunk 46 optimal weight: 0.0670 chunk 109 optimal weight: 1.9990 overall best weight: 0.2274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2186 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= 0.211 Angle : 0.819 7.528 17340 Z= 0.438 Chirality : 0.045 0.130 1950 Planarity : 0.003 0.017 2295 Dihedral : 5.953 22.214 1695 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 3.88 % Allowed : 20.39 % Favored : 75.73 % 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: -4.34 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.80 (0.43), residues: 180 loop : -3.41 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS G 10 PHE 0.005 0.001 PHE I 54 TYR 0.012 0.002 TYR L 76 ARG 0.000 0.000 ARG J 66 *********************** 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 17 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.099 Fit side-chains revert: symmetry clash REVERT: A 76 TYR cc_start: 0.8716 (p90) cc_final: 0.8490 (p90) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0846 time to fit residues: 1.7297 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 : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 4.9990 chunk 102 optimal weight: 0.0170 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 136 optimal weight: 0.0770 chunk 144 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 129 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.1960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2480 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= 0.207 Angle : 0.797 6.338 17340 Z= 0.425 Chirality : 0.045 0.132 1950 Planarity : 0.003 0.014 2295 Dihedral : 5.878 21.925 1695 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 3.88 % Allowed : 21.36 % Favored : 74.76 % 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: -4.36 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.74 (0.42), residues: 180 loop : -3.44 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 36 PHE 0.005 0.001 PHE D 9 TYR 0.010 0.001 TYR L 76 ARG 0.000 0.000 ARG B 28 *********************** REFINEMENT MACRO_CYCLE 4 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 17 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: G 76 TYR cc_start: 0.8215 (p90) cc_final: 0.7947 (p90) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1017 time to fit residues: 1.9897 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 : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 12705 Z= 0.381 Angle : 0.933 8.556 17340 Z= 0.496 Chirality : 0.050 0.155 1950 Planarity : 0.005 0.017 2295 Dihedral : 6.543 22.197 1695 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 31.24 Ramachandran Plot: Outliers : 3.88 % Allowed : 28.16 % Favored : 67.96 % 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: -5.12 (0.20), residues: 1545 helix: None (None), residues: 0 sheet: -2.69 (0.23), residues: 585 loop : -4.10 (0.17), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS H 36 PHE 0.014 0.003 PHE J 22 TYR 0.016 0.003 TYR O 84 ARG 0.003 0.001 ARG D 25 *********************** 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 10 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.102 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0855 time to fit residues: 1.0888 Evaluate side-chains 8 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 0.0980 chunk 76 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3228 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= 0.224 Angle : 0.853 7.220 17340 Z= 0.452 Chirality : 0.048 0.139 1950 Planarity : 0.003 0.016 2295 Dihedral : 6.291 21.425 1695 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 21.17 Ramachandran Plot: Outliers : 3.88 % Allowed : 22.33 % Favored : 73.79 % 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: -4.73 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.16 (0.34), residues: 255 loop : -3.73 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 36 PHE 0.006 0.001 PHE E 7 TYR 0.007 0.001 TYR G 84 ARG 0.001 0.000 ARG I 25 *********************** REFINEMENT MACRO_CYCLE 6 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 : 0.105 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0793 time to fit residues: 1.2877 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 : 0.112 ------------------------------------------------------------------------------- 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: 4.9990 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 122 optimal weight: 0.0170 chunk 81 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 overall best weight: 0.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12705 Z= 0.214 Angle : 0.873 11.226 17340 Z= 0.467 Chirality : 0.045 0.138 1950 Planarity : 0.003 0.016 2295 Dihedral : 6.032 20.046 1695 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 3.88 % Allowed : 24.27 % Favored : 71.84 % 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: -4.90 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.71 (0.26), residues: 390 loop : -3.77 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS K 36 PHE 0.006 0.001 PHE B 9 TYR 0.023 0.002 TYR I 76 ARG 0.001 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 7 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 17 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.105 Fit side-chains REVERT: A 59 GLU cc_start: 0.7384 (mp0) cc_final: 0.6854 (mp0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0821 time to fit residues: 1.6786 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 : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.0870 chunk 13 optimal weight: 0.0030 chunk 113 optimal weight: 0.0020 chunk 131 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3500 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= 0.227 Angle : 0.891 9.378 17340 Z= 0.471 Chirality : 0.046 0.142 1950 Planarity : 0.004 0.018 2295 Dihedral : 6.157 18.767 1695 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 14.84 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: -4.92 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.83 (0.26), residues: 390 loop : -3.74 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS D 10 PHE 0.005 0.001 PHE O 88 TYR 0.025 0.002 TYR I 76 ARG 0.001 0.000 ARG E 66 *********************** 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 : 0.093 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0685 time to fit residues: 1.2720 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 : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.0270 chunk 41 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 127 optimal weight: 0.3980 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 0.3980 chunk 86 optimal weight: 0.0060 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3901 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= 0.221 Angle : 0.886 8.763 17340 Z= 0.463 Chirality : 0.047 0.139 1950 Planarity : 0.004 0.019 2295 Dihedral : 6.153 19.442 1695 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 4.85 % Allowed : 21.36 % Favored : 73.79 % 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: -4.80 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.81 (0.27), residues: 360 loop : -3.63 (0.16), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 36 PHE 0.005 0.001 PHE H 54 TYR 0.026 0.002 TYR I 76 ARG 0.000 0.000 ARG M 28 *********************** 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 12 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.100 Fit side-chains REVERT: A 46 MET cc_start: 0.7651 (mmp) cc_final: 0.7432 (mmm) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0761 time to fit residues: 1.1467 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 137 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 91 optimal weight: 0.0070 chunk 72 optimal weight: 0.0070 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 0.0670 chunk 36 optimal weight: 0.0030 overall best weight: 0.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4495 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= 0.225 Angle : 0.858 8.449 17340 Z= 0.448 Chirality : 0.047 0.143 1950 Planarity : 0.004 0.019 2295 Dihedral : 5.755 18.872 1695 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 4.85 % Allowed : 15.53 % Favored : 79.61 % 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: -4.89 (0.18), residues: 1545 helix: None (None), residues: 0 sheet: -3.17 (0.26), residues: 330 loop : -3.59 (0.15), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 36 PHE 0.007 0.001 PHE H 7 TYR 0.024 0.002 TYR H 76 ARG 0.001 0.000 ARG D 66 ********************** 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 15 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.104 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0729 time to fit residues: 1.3525 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 : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 0.0060 chunk 86 optimal weight: 0.0470 overall best weight: 0.2494 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.062082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.055043 restraints weight = 7060.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.056187 restraints weight = 4871.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.057061 restraints weight = 3645.039| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4486 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= 0.201 Angle : 0.797 8.278 17340 Z= 0.419 Chirality : 0.046 0.158 1950 Planarity : 0.003 0.018 2295 Dihedral : 5.511 19.697 1695 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 14.00 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: -4.75 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -3.16 (0.26), residues: 330 loop : -3.46 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 36 PHE 0.004 0.001 PHE A 7 TYR 0.025 0.002 TYR H 76 ARG 0.001 0.000 ARG G 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.09 seconds wall clock time: 46 minutes 47.95 seconds (2807.95 seconds total)