Starting phenix.real_space_refine on Wed Sep 17 23:46:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cod_45776/09_2025/9cod_45776.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cod_45776/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cod_45776/09_2025/9cod_45776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cod_45776/09_2025/9cod_45776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cod_45776/09_2025/9cod_45776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cod_45776/09_2025/9cod_45776.map" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 7800 2.51 5 N 1890 2.21 5 O 2625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12405 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 827 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O Time building chain proxies: 1.27, per 1000 atoms: 0.10 Number of scatterers: 12405 At special positions: 0 Unit cell: (187.04, 185.92, 51.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2625 8.00 N 1890 7.00 C 7800 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 527.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3030 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 30 sheets defined 0.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR A 44 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL A 24 " --> pdb=" O TYR A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY A 30 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL A 38 " --> pdb=" O GLY A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR B 44 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL B 24 " --> pdb=" O TYR B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY B 30 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL B 38 " --> pdb=" O GLY B 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR C 44 " --> pdb=" O VAL C 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL C 24 " --> pdb=" O TYR C 44 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY C 30 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL C 38 " --> pdb=" O GLY C 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR D 44 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL D 24 " --> pdb=" O TYR D 44 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY D 30 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 38 " --> pdb=" O GLY D 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'E' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR E 44 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL E 24 " --> pdb=" O TYR E 44 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY E 30 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E 38 " --> pdb=" O GLY E 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'F' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR F 44 " --> pdb=" O VAL F 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL F 24 " --> pdb=" O TYR F 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY F 30 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL F 38 " --> pdb=" O GLY F 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'G' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR G 44 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL G 24 " --> pdb=" O TYR G 44 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY G 30 " --> pdb=" O VAL G 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL G 38 " --> pdb=" O GLY G 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'H' and resid 43 through 44 removed outlier: 3.657A pdb=" N TYR H 44 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL H 24 " --> pdb=" O TYR H 44 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY H 30 " --> pdb=" O VAL H 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 38 " --> pdb=" O GLY H 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'I' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR I 44 " --> pdb=" O VAL I 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL I 24 " --> pdb=" O TYR I 44 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY I 30 " --> pdb=" O VAL I 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL I 38 " --> pdb=" O GLY I 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'J' and resid 43 through 44 removed outlier: 3.659A pdb=" N TYR J 44 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL J 24 " --> pdb=" O TYR J 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY J 30 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL J 38 " --> pdb=" O GLY J 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR K 44 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL K 24 " --> pdb=" O TYR K 44 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY K 30 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL K 38 " --> pdb=" O GLY K 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'L' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR L 44 " --> pdb=" O VAL L 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL L 24 " --> pdb=" O TYR L 44 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.794A pdb=" N GLY L 30 " --> pdb=" O VAL L 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL L 38 " --> pdb=" O GLY L 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'M' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR M 44 " --> pdb=" O VAL M 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL M 24 " --> pdb=" O TYR M 44 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY M 30 " --> pdb=" O VAL M 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL M 38 " --> pdb=" O GLY M 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'N' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR N 44 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL N 24 " --> pdb=" O TYR N 44 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY N 30 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL N 38 " --> pdb=" O GLY N 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'O' and resid 43 through 44 removed outlier: 3.658A pdb=" N TYR O 44 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL O 24 " --> pdb=" O TYR O 44 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 30 through 31 removed outlier: 3.793A pdb=" N GLY O 30 " --> pdb=" O VAL O 38 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL O 38 " --> pdb=" O GLY O 30 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 90 hydrogen bonds defined for protein. 225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.31 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: 0.05 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: 12.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.070 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.910 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.85 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -3.26 (0.25), residues: 375 loop : -3.50 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 25 TYR 0.026 0.003 TYR B 76 PHE 0.007 0.002 PHE F 7 HIS 0.009 0.006 HIS C 10 Details of bonding type rmsd covalent geometry : bond 0.00372 (12705) covalent geometry : angle 1.08153 (17340) hydrogen bonds : bond 0.20624 ( 90) hydrogen bonds : angle 7.74721 ( 225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0464 time to fit residues: 0.9907 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 : 0.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.0070 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 0.3980 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 HIS A 19 ASN A 36 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.061186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.054152 restraints weight = 7701.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.055327 restraints weight = 5222.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.056274 restraints weight = 3896.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.056851 restraints weight = 3023.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.057318 restraints weight = 2474.762| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12705 Z= 0.167 Angle : 0.870 6.226 17340 Z= 0.462 Chirality : 0.049 0.154 1950 Planarity : 0.004 0.017 2295 Dihedral : 6.156 22.367 1695 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 3.88 % Allowed : 24.27 % Favored : 71.84 % Rotamer: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.82 (0.20), residues: 1545 helix: None (None), residues: 0 sheet: -3.39 (0.25), residues: 390 loop : -3.40 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 66 TYR 0.016 0.003 TYR D 76 PHE 0.003 0.001 PHE L 7 HIS 0.008 0.004 HIS M 10 Details of bonding type rmsd covalent geometry : bond 0.00353 (12705) covalent geometry : angle 0.87019 (17340) hydrogen bonds : bond 0.01481 ( 90) hydrogen bonds : angle 4.91962 ( 225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3090 Ramachandran restraints generated. 1545 Oldfield, 0 Emsley, 1545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.032 Fit side-chains REVERT: A 31 MET cc_start: 0.8290 (mpp) cc_final: 0.7971 (mpp) REVERT: A 76 TYR cc_start: 0.8615 (p90) cc_final: 0.8363 (p90) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0501 time to fit residues: 0.8012 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 : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 142 optimal weight: 0.0570 chunk 39 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 overall best weight: 0.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 10 HIS ** G 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.057243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.051350 restraints weight = 7124.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.052453 restraints weight = 4765.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.053169 restraints weight = 3447.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.053818 restraints weight = 2707.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054109 restraints weight = 2153.002| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 12705 Z= 0.164 Angle : 0.849 7.187 17340 Z= 0.452 Chirality : 0.045 0.125 1950 Planarity : 0.004 0.017 2295 Dihedral : 6.677 22.506 1695 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 3.88 % Allowed : 23.30 % Favored : 72.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.80 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.25 (0.34), residues: 255 loop : -3.78 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 28 TYR 0.010 0.002 TYR H 76 PHE 0.027 0.002 PHE O 22 HIS 0.005 0.003 HIS E 10 Details of bonding type rmsd covalent geometry : bond 0.00353 (12705) covalent geometry : angle 0.84894 (17340) hydrogen bonds : bond 0.01559 ( 90) hydrogen bonds : angle 5.24744 ( 225) *********************** REFINEMENT MACRO_CYCLE 3 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 11 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0553 time to fit residues: 0.6948 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 : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 0.8980 chunk 133 optimal weight: 0.4980 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 0.0060 chunk 46 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 21 optimal weight: 0.0170 chunk 20 optimal weight: 2.9990 chunk 143 optimal weight: 0.2980 chunk 44 optimal weight: 3.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- 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 = 0.3246 r_free = 0.3246 target = 0.058316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052638 restraints weight = 7537.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.053722 restraints weight = 4935.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054248 restraints weight = 3481.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.054945 restraints weight = 2777.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055397 restraints weight = 2195.028| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12705 Z= 0.153 Angle : 0.800 6.222 17340 Z= 0.423 Chirality : 0.045 0.129 1950 Planarity : 0.003 0.017 2295 Dihedral : 6.321 22.329 1695 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 3.88 % Allowed : 23.30 % Favored : 72.82 % Rotamer: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.73 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.16 (0.33), residues: 255 loop : -3.74 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 66 TYR 0.007 0.001 TYR E 44 PHE 0.012 0.002 PHE D 22 HIS 0.007 0.004 HIS J 10 Details of bonding type rmsd covalent geometry : bond 0.00327 (12705) covalent geometry : angle 0.80023 (17340) hydrogen bonds : bond 0.01215 ( 90) hydrogen bonds : angle 4.90970 ( 225) *********************** 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 13 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.034 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0327 time to fit residues: 0.5126 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 : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 53 optimal weight: 0.0050 chunk 94 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 5 optimal weight: 0.0470 chunk 103 optimal weight: 0.0870 chunk 22 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.3070 ------------------------------------------------------------------------------- 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 = 0.3269 r_free = 0.3269 target = 0.058650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.052181 restraints weight = 7643.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053268 restraints weight = 5196.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054061 restraints weight = 3835.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054674 restraints weight = 2968.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.055046 restraints weight = 2398.746| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3267 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= 0.149 Angle : 0.821 9.121 17340 Z= 0.435 Chirality : 0.045 0.129 1950 Planarity : 0.003 0.017 2295 Dihedral : 6.351 22.091 1695 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.58 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.82 (0.18), residues: 1545 helix: None (None), residues: 0 sheet: -2.17 (0.33), residues: 255 loop : -3.82 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 28 TYR 0.007 0.001 TYR H 84 PHE 0.008 0.001 PHE M 22 HIS 0.005 0.003 HIS J 10 Details of bonding type rmsd covalent geometry : bond 0.00314 (12705) covalent geometry : angle 0.82107 (17340) hydrogen bonds : bond 0.01285 ( 90) hydrogen bonds : angle 4.74818 ( 225) *********************** 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 13 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.032 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0268 time to fit residues: 0.4420 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 : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 143 optimal weight: 0.1980 chunk 112 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 chunk 123 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 56 optimal weight: 0.0060 chunk 22 optimal weight: 0.0040 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.0470 overall best weight: 0.1306 ------------------------------------------------------------------------------- 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 = 0.060188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.053780 restraints weight = 7648.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054920 restraints weight = 5142.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.055797 restraints weight = 3717.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056429 restraints weight = 2847.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.056859 restraints weight = 2289.826| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3435 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= 0.155 Angle : 0.820 7.572 17340 Z= 0.431 Chirality : 0.045 0.130 1950 Planarity : 0.003 0.016 2295 Dihedral : 6.194 20.166 1695 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 3.88 % Allowed : 20.39 % Favored : 75.73 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.57 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.66 (0.43), residues: 180 loop : -3.63 (0.14), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 28 TYR 0.006 0.001 TYR H 84 PHE 0.007 0.001 PHE G 22 HIS 0.007 0.004 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00321 (12705) covalent geometry : angle 0.81975 (17340) hydrogen bonds : bond 0.01477 ( 90) hydrogen bonds : angle 4.60860 ( 225) *********************** 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 16 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.036 Fit side-chains REVERT: G 31 MET cc_start: 0.8283 (mpp) cc_final: 0.7845 (mpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0379 time to fit residues: 0.7036 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 : 0.031 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.3980 chunk 51 optimal weight: 0.0870 chunk 25 optimal weight: 0.4980 chunk 124 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 114 optimal weight: 0.0470 chunk 128 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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 = 0.3328 r_free = 0.3328 target = 0.061783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.053641 restraints weight = 7005.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054680 restraints weight = 5134.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055506 restraints weight = 4076.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.056141 restraints weight = 3358.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.056593 restraints weight = 2826.556| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4047 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= 0.160 Angle : 0.868 8.318 17340 Z= 0.460 Chirality : 0.045 0.129 1950 Planarity : 0.003 0.017 2295 Dihedral : 6.809 20.309 1695 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 3.88 % Allowed : 19.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.60 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.92 (0.41), residues: 180 loop : -3.62 (0.15), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 28 TYR 0.008 0.001 TYR M 44 PHE 0.005 0.001 PHE I 22 HIS 0.006 0.003 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00336 (12705) covalent geometry : angle 0.86776 (17340) hydrogen bonds : bond 0.01186 ( 90) hydrogen bonds : angle 4.71793 ( 225) *********************** 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 16 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.020 Fit side-chains REVERT: A 31 MET cc_start: 0.8194 (mpp) cc_final: 0.7896 (mpp) REVERT: A 59 GLU cc_start: 0.7276 (mp0) cc_final: 0.6713 (mp0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0321 time to fit residues: 0.6044 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 : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.3980 chunk 51 optimal weight: 0.0670 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 overall best weight: 0.3916 ------------------------------------------------------------------------------- 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 = 0.061307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.053135 restraints weight = 7825.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.054217 restraints weight = 5740.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.054998 restraints weight = 4470.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.055633 restraints weight = 3652.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.056064 restraints weight = 3100.374| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4021 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= 0.156 Angle : 0.921 10.414 17340 Z= 0.485 Chirality : 0.045 0.128 1950 Planarity : 0.004 0.028 2295 Dihedral : 6.717 22.136 1695 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.67 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.36 (0.30), residues: 255 loop : -3.63 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 25 TYR 0.024 0.002 TYR F 76 PHE 0.005 0.001 PHE I 22 HIS 0.006 0.003 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00333 (12705) covalent geometry : angle 0.92095 (17340) hydrogen bonds : bond 0.01184 ( 90) hydrogen bonds : angle 4.72921 ( 225) *********************** 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 14 residues out of total 95 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.031 Fit side-chains REVERT: C 90 VAL cc_start: 0.8983 (t) cc_final: 0.8271 (t) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0257 time to fit residues: 0.4538 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 : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 65 optimal weight: 0.2980 chunk 119 optimal weight: 0.0040 chunk 67 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.059867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.051815 restraints weight = 7794.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.052921 restraints weight = 5540.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.053756 restraints weight = 4262.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054378 restraints weight = 3453.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.054851 restraints weight = 2909.083| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.4395 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= 0.157 Angle : 0.904 10.012 17340 Z= 0.476 Chirality : 0.046 0.128 1950 Planarity : 0.004 0.021 2295 Dihedral : 6.695 20.305 1695 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 4.85 % Allowed : 20.39 % Favored : 74.76 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.49 (0.20), residues: 1545 helix: None (None), residues: 0 sheet: -2.10 (0.39), residues: 180 loop : -3.49 (0.16), residues: 1365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 28 TYR 0.025 0.002 TYR H 76 PHE 0.004 0.001 PHE B 9 HIS 0.006 0.003 HIS K 36 Details of bonding type rmsd covalent geometry : bond 0.00328 (12705) covalent geometry : angle 0.90350 (17340) hydrogen bonds : bond 0.01300 ( 90) hydrogen bonds : angle 4.41516 ( 225) *********************** 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 : 0.036 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0273 time to fit residues: 0.4819 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 : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 11 optimal weight: 2.9990 chunk 145 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 0.0370 chunk 124 optimal weight: 0.0270 chunk 97 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 22 optimal weight: 0.0980 chunk 117 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 = 0.061841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053866 restraints weight = 7373.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.054856 restraints weight = 5538.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.055596 restraints weight = 4410.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.056136 restraints weight = 3682.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.056535 restraints weight = 3208.059| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.4691 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= 0.155 Angle : 0.928 9.827 17340 Z= 0.475 Chirality : 0.046 0.134 1950 Planarity : 0.004 0.019 2295 Dihedral : 6.468 19.488 1695 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 5.83 % Allowed : 18.45 % Favored : 75.73 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.51 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -1.71 (0.45), residues: 150 loop : -3.55 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 66 TYR 0.025 0.002 TYR H 76 PHE 0.005 0.001 PHE N 88 HIS 0.009 0.004 HIS I 10 Details of bonding type rmsd covalent geometry : bond 0.00327 (12705) covalent geometry : angle 0.92804 (17340) hydrogen bonds : bond 0.01167 ( 90) hydrogen bonds : angle 4.70652 ( 225) ********************** 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 : 0.040 Fit side-chains REVERT: C 65 TYR cc_start: 0.8806 (m-10) cc_final: 0.8338 (m-10) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0236 time to fit residues: 0.3885 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 : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 118 optimal weight: 1.9990 chunk 44 optimal weight: 0.0020 chunk 149 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.5804 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.060719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.053212 restraints weight = 7697.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.054220 restraints weight = 5605.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.054907 restraints weight = 4371.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.055452 restraints weight = 3630.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055512 restraints weight = 3128.090| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4762 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= 0.154 Angle : 0.894 9.541 17340 Z= 0.468 Chirality : 0.045 0.127 1950 Planarity : 0.004 0.018 2295 Dihedral : 6.372 19.588 1695 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 5.83 % Allowed : 20.39 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.58 (0.19), residues: 1545 helix: None (None), residues: 0 sheet: -2.07 (0.33), residues: 225 loop : -3.60 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 25 TYR 0.025 0.002 TYR H 76 PHE 0.004 0.001 PHE I 9 HIS 0.008 0.003 HIS I 10 Details of bonding type rmsd covalent geometry : bond 0.00327 (12705) covalent geometry : angle 0.89387 (17340) hydrogen bonds : bond 0.01349 ( 90) hydrogen bonds : angle 4.93798 ( 225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1221.29 seconds wall clock time: 22 minutes 18.68 seconds (1338.68 seconds total)