Starting phenix.real_space_refine on Wed Mar 5 17:11:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owk_17239/03_2025/8owk_17239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owk_17239/03_2025/8owk_17239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8owk_17239/03_2025/8owk_17239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owk_17239/03_2025/8owk_17239.map" model { file = "/net/cci-nas-00/data/ceres_data/8owk_17239/03_2025/8owk_17239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owk_17239/03_2025/8owk_17239.cif" } resolution = 3.86 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= 0.001 sd= 0.006 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 10 5.16 5 C 1940 2.51 5 N 530 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3050 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 305 Classifications: {'peptide': 40} Link IDs: {'TRANS': 39} Restraints were copied for chains: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.62, per 1000 atoms: 0.53 Number of scatterers: 3050 At special positions: 0 Unit cell: (89.25, 120.75, 42, 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 10 16.00 O 570 8.00 N 530 7.00 C 1940 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: 0.71 Conformation dependent library (CDL) restraints added in 390.6 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 67.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 23 removed outlier: 6.766A pdb=" N TYR C 10 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU B 11 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL C 12 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS B 13 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR A 10 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU C 11 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 12 " --> pdb=" O GLU C 11 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS C 13 " --> pdb=" O VAL A 12 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR D 10 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU A 11 " --> pdb=" O TYR D 10 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 12 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS A 13 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU D 3 " --> pdb=" O PHE E 4 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS E 6 " --> pdb=" O GLU D 3 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG D 5 " --> pdb=" O HIS E 6 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER E 8 " --> pdb=" O ARG D 5 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP D 7 " --> pdb=" O SER E 8 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR E 10 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY D 9 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N VAL E 12 " --> pdb=" O GLY D 9 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLU D 11 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N HIS E 14 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS D 13 " --> pdb=" O HIS E 14 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYS E 16 " --> pdb=" O HIS D 13 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN D 15 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL E 18 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE E 20 " --> pdb=" O LEU D 17 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE D 19 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLU E 22 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA D 21 " --> pdb=" O GLU E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 36 removed outlier: 6.876A pdb=" N ALA C 30 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE B 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE C 32 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY B 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N ALA A 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N GLY C 33 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N MET C 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU A 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA D 30 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE A 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D 32 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLY A 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA E 30 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE D 31 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE E 32 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY D 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 3 through 23 removed outlier: 6.766A pdb=" N TYR H 10 " --> pdb=" O GLY G 9 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU G 11 " --> pdb=" O TYR H 10 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL H 12 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS G 13 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR F 10 " --> pdb=" O GLY H 9 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU H 11 " --> pdb=" O TYR F 10 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL F 12 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS H 13 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU F 3 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N HIS I 6 " --> pdb=" O GLU F 3 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG F 5 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N SER I 8 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASP F 7 " --> pdb=" O SER I 8 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N TYR I 10 " --> pdb=" O ASP F 7 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLY F 9 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N VAL I 12 " --> pdb=" O GLY F 9 " (cutoff:3.500A) removed outlier: 8.689A pdb=" N GLU F 11 " --> pdb=" O VAL I 12 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N HIS I 14 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS F 13 " --> pdb=" O HIS I 14 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LYS I 16 " --> pdb=" O HIS F 13 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N GLN F 15 " --> pdb=" O LYS I 16 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL I 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU F 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE I 20 " --> pdb=" O LEU F 17 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N PHE F 19 " --> pdb=" O PHE I 20 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU I 22 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA F 21 " --> pdb=" O GLU I 22 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU I 3 " --> pdb=" O PHE J 4 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N HIS J 6 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG I 5 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N SER J 8 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP I 7 " --> pdb=" O SER J 8 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N TYR J 10 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY I 9 " --> pdb=" O TYR J 10 " (cutoff:3.500A) removed outlier: 10.199A pdb=" N VAL J 12 " --> pdb=" O GLY I 9 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N GLU I 11 " --> pdb=" O VAL J 12 " (cutoff:3.500A) removed outlier: 8.817A pdb=" N HIS J 14 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS I 13 " --> pdb=" O HIS J 14 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LYS J 16 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N GLN I 15 " --> pdb=" O LYS J 16 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL J 18 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU I 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N PHE J 20 " --> pdb=" O LEU I 17 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N PHE I 19 " --> pdb=" O PHE J 20 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N GLU J 22 " --> pdb=" O PHE I 19 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA I 21 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 29 through 36 removed outlier: 6.876A pdb=" N ALA H 30 " --> pdb=" O GLY G 29 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE G 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE H 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY G 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ALA F 30 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 9.777A pdb=" N GLY H 33 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE F 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N MET H 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU F 34 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA I 30 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE F 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ILE I 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLY F 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA J 30 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ILE I 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE J 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N GLY I 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) 98 hydrogen bonds defined for protein. 294 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: 0.74 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 950 1.33 - 1.44: 492 1.44 - 1.56: 1648 1.56 - 1.67: 0 1.67 - 1.79: 20 Bond restraints: 3110 Sorted by residual: bond pdb=" CA HIS B 6 " pdb=" C HIS B 6 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.19e-02 7.06e+03 1.44e+01 bond pdb=" CA HIS G 6 " pdb=" C HIS G 6 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.19e-02 7.06e+03 1.44e+01 bond pdb=" CA HIS C 6 " pdb=" C HIS C 6 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.19e-02 7.06e+03 1.44e+01 bond pdb=" CA HIS H 6 " pdb=" C HIS H 6 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.19e-02 7.06e+03 1.44e+01 bond pdb=" CA HIS F 6 " pdb=" C HIS F 6 " ideal model delta sigma weight residual 1.521 1.476 0.045 1.19e-02 7.06e+03 1.43e+01 ... (remaining 3105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.45: 4050 6.45 - 12.90: 92 12.90 - 19.35: 18 19.35 - 25.80: 0 25.80 - 32.25: 10 Bond angle restraints: 4170 Sorted by residual: angle pdb=" N GLY I 25 " pdb=" CA GLY I 25 " pdb=" C GLY I 25 " ideal model delta sigma weight residual 111.36 143.61 -32.25 1.17e+00 7.31e-01 7.60e+02 angle pdb=" N GLY D 25 " pdb=" CA GLY D 25 " pdb=" C GLY D 25 " ideal model delta sigma weight residual 111.36 143.61 -32.25 1.17e+00 7.31e-01 7.60e+02 angle pdb=" N GLY A 25 " pdb=" CA GLY A 25 " pdb=" C GLY A 25 " ideal model delta sigma weight residual 111.36 143.61 -32.25 1.17e+00 7.31e-01 7.60e+02 angle pdb=" N GLY C 25 " pdb=" CA GLY C 25 " pdb=" C GLY C 25 " ideal model delta sigma weight residual 111.36 143.60 -32.24 1.17e+00 7.31e-01 7.59e+02 angle pdb=" N GLY H 25 " pdb=" CA GLY H 25 " pdb=" C GLY H 25 " ideal model delta sigma weight residual 111.36 143.60 -32.24 1.17e+00 7.31e-01 7.59e+02 ... (remaining 4165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.42: 1425 7.42 - 14.85: 285 14.85 - 22.27: 10 22.27 - 29.70: 10 29.70 - 37.12: 10 Dihedral angle restraints: 1740 sinusoidal: 660 harmonic: 1080 Sorted by residual: dihedral pdb=" N ILE E 32 " pdb=" C ILE E 32 " pdb=" CA ILE E 32 " pdb=" CB ILE E 32 " ideal model delta harmonic sigma weight residual 123.40 115.41 7.99 0 2.50e+00 1.60e-01 1.02e+01 dihedral pdb=" N ILE J 32 " pdb=" C ILE J 32 " pdb=" CA ILE J 32 " pdb=" CB ILE J 32 " ideal model delta harmonic sigma weight residual 123.40 115.41 7.99 0 2.50e+00 1.60e-01 1.02e+01 dihedral pdb=" N ILE A 32 " pdb=" C ILE A 32 " pdb=" CA ILE A 32 " pdb=" CB ILE A 32 " ideal model delta harmonic sigma weight residual 123.40 115.46 7.94 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 1737 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.056: 150 0.056 - 0.110: 125 0.110 - 0.165: 95 0.165 - 0.220: 30 0.220 - 0.275: 40 Chirality restraints: 440 Sorted by residual: chirality pdb=" CG LEU C 17 " pdb=" CB LEU C 17 " pdb=" CD1 LEU C 17 " pdb=" CD2 LEU C 17 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU H 17 " pdb=" CB LEU H 17 " pdb=" CD1 LEU H 17 " pdb=" CD2 LEU H 17 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU J 17 " pdb=" CB LEU J 17 " pdb=" CD1 LEU J 17 " pdb=" CD2 LEU J 17 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 437 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 19 " 0.023 2.00e-02 2.50e+03 1.91e-02 6.41e+00 pdb=" CG PHE C 19 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 19 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 19 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 19 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 19 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE C 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 19 " -0.023 2.00e-02 2.50e+03 1.91e-02 6.41e+00 pdb=" CG PHE H 19 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE H 19 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE H 19 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE H 19 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 19 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE H 19 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 19 " 0.023 2.00e-02 2.50e+03 1.90e-02 6.31e+00 pdb=" CG PHE A 19 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 19 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 19 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 19 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 19 " 0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 19 " -0.001 2.00e-02 2.50e+03 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 1772 2.99 - 3.47: 2833 3.47 - 3.94: 5149 3.94 - 4.42: 5764 4.42 - 4.90: 11141 Nonbonded interactions: 26659 Sorted by model distance: nonbonded pdb=" O ASP A 1 " pdb=" OE1 GLU A 3 " model vdw 2.508 3.040 nonbonded pdb=" O ASP F 1 " pdb=" OE1 GLU F 3 " model vdw 2.509 3.040 nonbonded pdb=" O ASP C 1 " pdb=" OE1 GLU C 3 " model vdw 2.509 3.040 nonbonded pdb=" O ASP H 1 " pdb=" OE1 GLU H 3 " model vdw 2.509 3.040 nonbonded pdb=" O ASP J 1 " pdb=" OE1 GLU J 3 " model vdw 2.510 3.040 ... (remaining 26654 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.950 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 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 : 0.013 0.045 3110 Z= 0.855 Angle : 3.090 32.249 4170 Z= 2.193 Chirality : 0.121 0.275 440 Planarity : 0.008 0.022 550 Dihedral : 7.402 37.119 1060 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.23 % Allowed : 6.45 % Favored : 90.32 % 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: 0.74 (0.43), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.58 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS G 6 PHE 0.039 0.012 PHE C 19 TYR 0.042 0.010 TYR G 10 ARG 0.002 0.001 ARG C 5 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 3 GLU cc_start: 0.5564 (mp0) cc_final: 0.4830 (tm-30) REVERT: B 16 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.7043 (ttpt) REVERT: E 19 PHE cc_start: 0.7706 (m-80) cc_final: 0.7343 (m-80) REVERT: G 3 GLU cc_start: 0.5571 (mp0) cc_final: 0.4837 (tm-30) REVERT: G 16 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.7049 (ttpt) REVERT: J 19 PHE cc_start: 0.7700 (m-80) cc_final: 0.7336 (m-80) REVERT: J 23 ASP cc_start: 0.6333 (t0) cc_final: 0.6126 (t0) outliers start: 10 outliers final: 0 residues processed: 150 average time/residue: 0.1510 time to fit residues: 26.8551 Evaluate side-chains 99 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 LYS Chi-restraints excluded: chain G residue 16 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS C 6 HIS D 6 HIS E 6 HIS F 6 HIS H 6 HIS I 6 HIS J 6 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.106913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.087167 restraints weight = 5570.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.089497 restraints weight = 2269.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.090960 restraints weight = 1476.666| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3110 Z= 0.267 Angle : 0.809 7.978 4170 Z= 0.415 Chirality : 0.054 0.159 440 Planarity : 0.003 0.014 550 Dihedral : 6.692 19.433 418 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.23 % Allowed : 12.90 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.36), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.27), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 14 PHE 0.013 0.003 PHE D 19 TYR 0.016 0.003 TYR F 10 ARG 0.003 0.001 ARG J 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 106 average time/residue: 0.1293 time to fit residues: 16.8015 Evaluate side-chains 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 23 optimal weight: 0.0050 chunk 17 optimal weight: 5.9990 overall best weight: 3.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS F 6 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.100078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.080493 restraints weight = 5549.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.082691 restraints weight = 2261.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.083980 restraints weight = 1469.294| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 3110 Z= 0.321 Angle : 0.714 8.295 4170 Z= 0.369 Chirality : 0.053 0.128 440 Planarity : 0.003 0.016 550 Dihedral : 5.554 16.501 410 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.58 % Allowed : 11.61 % Favored : 85.81 % 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: -2.24 (0.33), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS I 13 PHE 0.012 0.002 PHE I 4 TYR 0.014 0.003 TYR C 10 ARG 0.009 0.002 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 15 GLN cc_start: 0.8229 (tt0) cc_final: 0.7681 (mt0) outliers start: 8 outliers final: 2 residues processed: 83 average time/residue: 0.1189 time to fit residues: 12.4234 Evaluate side-chains 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 0.0030 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 4.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS F 6 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.095977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.076608 restraints weight = 5946.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.078593 restraints weight = 2381.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.079681 restraints weight = 1566.200| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 3110 Z= 0.372 Angle : 0.672 7.451 4170 Z= 0.358 Chirality : 0.054 0.133 440 Planarity : 0.003 0.020 550 Dihedral : 5.379 12.834 410 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.58 % Allowed : 10.97 % Favored : 86.45 % 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: -2.58 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS F 13 PHE 0.010 0.002 PHE F 19 TYR 0.013 0.002 TYR H 10 ARG 0.010 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.344 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 83 average time/residue: 0.0893 time to fit residues: 9.8261 Evaluate side-chains 73 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 HIS ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS F 6 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.096972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.076960 restraints weight = 5845.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.078930 restraints weight = 2368.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.079991 restraints weight = 1575.065| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.5842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3110 Z= 0.290 Angle : 0.634 8.562 4170 Z= 0.328 Chirality : 0.052 0.132 440 Planarity : 0.003 0.017 550 Dihedral : 5.023 15.427 410 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.26 % Allowed : 13.87 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.24), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 13 PHE 0.012 0.002 PHE C 20 TYR 0.010 0.002 TYR I 10 ARG 0.007 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.351 Fit side-chains REVERT: B 3 GLU cc_start: 0.6664 (mp0) cc_final: 0.5865 (tm-30) REVERT: C 3 GLU cc_start: 0.6424 (mp0) cc_final: 0.5628 (tm-30) REVERT: G 3 GLU cc_start: 0.6512 (mp0) cc_final: 0.5635 (tm-30) outliers start: 7 outliers final: 3 residues processed: 77 average time/residue: 0.0925 time to fit residues: 9.6771 Evaluate side-chains 69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS F 6 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.092310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.073490 restraints weight = 6472.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075254 restraints weight = 2655.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.076168 restraints weight = 1751.092| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.6170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 3110 Z= 0.483 Angle : 0.720 8.098 4170 Z= 0.396 Chirality : 0.055 0.157 440 Planarity : 0.004 0.029 550 Dihedral : 5.570 14.684 410 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.94 % Allowed : 15.81 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.28), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.21), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS J 13 PHE 0.012 0.003 PHE B 19 TYR 0.011 0.002 TYR I 10 ARG 0.005 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 68 time to evaluate : 0.354 Fit side-chains REVERT: B 3 GLU cc_start: 0.6559 (mp0) cc_final: 0.5717 (tm-30) REVERT: C 3 GLU cc_start: 0.6577 (mp0) cc_final: 0.5579 (tm-30) REVERT: G 3 GLU cc_start: 0.6560 (mp0) cc_final: 0.5642 (tm-30) outliers start: 6 outliers final: 4 residues processed: 73 average time/residue: 0.0835 time to fit residues: 8.3807 Evaluate side-chains 67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain E residue 6 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain J residue 6 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.095047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.075378 restraints weight = 5977.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.077254 restraints weight = 2416.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.078252 restraints weight = 1598.069| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3110 Z= 0.294 Angle : 0.631 7.784 4170 Z= 0.336 Chirality : 0.052 0.148 440 Planarity : 0.003 0.018 550 Dihedral : 5.009 12.575 410 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.29 % Allowed : 16.13 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 13 PHE 0.009 0.002 PHE F 19 TYR 0.008 0.002 TYR H 10 ARG 0.005 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.330 Fit side-chains REVERT: B 3 GLU cc_start: 0.6561 (mp0) cc_final: 0.5789 (tm-30) REVERT: C 3 GLU cc_start: 0.6402 (mp0) cc_final: 0.5594 (tm-30) REVERT: G 3 GLU cc_start: 0.6571 (mp0) cc_final: 0.5800 (tm-30) REVERT: H 3 GLU cc_start: 0.6305 (mp0) cc_final: 0.5598 (tm-30) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 0.0844 time to fit residues: 8.6862 Evaluate side-chains 69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 0.0030 chunk 37 optimal weight: 4.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.093980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.074388 restraints weight = 6086.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.076098 restraints weight = 2601.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.076946 restraints weight = 1762.027| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3110 Z= 0.331 Angle : 0.644 7.423 4170 Z= 0.347 Chirality : 0.053 0.153 440 Planarity : 0.003 0.019 550 Dihedral : 4.999 11.583 410 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.29 % Allowed : 15.16 % Favored : 83.55 % 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: -3.15 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.003 HIS F 13 PHE 0.012 0.002 PHE C 20 TYR 0.007 0.002 TYR H 10 ARG 0.004 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.362 Fit side-chains REVERT: B 3 GLU cc_start: 0.6504 (mp0) cc_final: 0.5744 (tm-30) REVERT: C 3 GLU cc_start: 0.6252 (mp0) cc_final: 0.5524 (tm-30) REVERT: G 3 GLU cc_start: 0.6374 (mp0) cc_final: 0.5576 (tm-30) REVERT: H 3 GLU cc_start: 0.6320 (mp0) cc_final: 0.5650 (tm-30) outliers start: 4 outliers final: 2 residues processed: 76 average time/residue: 0.0907 time to fit residues: 9.3981 Evaluate side-chains 72 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.098343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.077548 restraints weight = 5760.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.079458 restraints weight = 2336.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.080587 restraints weight = 1562.258| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 3110 Z= 0.175 Angle : 0.582 7.074 4170 Z= 0.302 Chirality : 0.052 0.142 440 Planarity : 0.002 0.007 550 Dihedral : 4.523 11.364 410 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.29 % Allowed : 16.45 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 13 PHE 0.015 0.002 PHE F 20 TYR 0.006 0.001 TYR I 10 ARG 0.003 0.001 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.359 Fit side-chains REVERT: B 3 GLU cc_start: 0.6659 (mp0) cc_final: 0.5875 (tm-30) REVERT: B 5 ARG cc_start: 0.7247 (ttm110) cc_final: 0.6513 (tpm170) REVERT: C 3 GLU cc_start: 0.6295 (mp0) cc_final: 0.5633 (tm-30) REVERT: G 3 GLU cc_start: 0.6632 (mp0) cc_final: 0.5856 (tm-30) REVERT: G 5 ARG cc_start: 0.7221 (ttm110) cc_final: 0.6511 (tpm170) REVERT: H 3 GLU cc_start: 0.6243 (mp0) cc_final: 0.5549 (tm-30) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.1198 time to fit residues: 11.3425 Evaluate side-chains 66 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain G residue 12 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.093187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.073531 restraints weight = 5997.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.075177 restraints weight = 2618.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.075989 restraints weight = 1792.488| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3110 Z= 0.369 Angle : 0.666 7.254 4170 Z= 0.365 Chirality : 0.053 0.155 440 Planarity : 0.004 0.045 550 Dihedral : 4.946 11.643 410 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.29 % Allowed : 17.10 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS F 13 PHE 0.019 0.003 PHE E 20 TYR 0.010 0.002 TYR J 10 ARG 0.016 0.001 ARG D 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.348 Fit side-chains REVERT: B 3 GLU cc_start: 0.6499 (mp0) cc_final: 0.5743 (tm-30) REVERT: C 3 GLU cc_start: 0.6284 (mp0) cc_final: 0.5567 (tm-30) REVERT: G 3 GLU cc_start: 0.6497 (mp0) cc_final: 0.5744 (tm-30) REVERT: G 5 ARG cc_start: 0.7284 (ttm110) cc_final: 0.6640 (tpm170) REVERT: H 3 GLU cc_start: 0.6243 (mp0) cc_final: 0.5578 (tm-30) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.1061 time to fit residues: 10.4264 Evaluate side-chains 75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain E residue 6 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain J residue 6 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.092646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.073222 restraints weight = 6210.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.074873 restraints weight = 2675.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.075854 restraints weight = 1820.504| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 3110 Z= 0.392 Angle : 0.683 7.200 4170 Z= 0.377 Chirality : 0.054 0.155 440 Planarity : 0.004 0.023 550 Dihedral : 5.149 15.340 410 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.65 % Allowed : 17.74 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS A 13 PHE 0.017 0.003 PHE E 20 TYR 0.012 0.002 TYR J 10 ARG 0.013 0.001 ARG D 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1179.50 seconds wall clock time: 21 minutes 8.43 seconds (1268.43 seconds total)