Starting phenix.real_space_refine on Mon Feb 10 22:14:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8owk_17239/02_2025/8owk_17239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8owk_17239/02_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_17239/02_2025/8owk_17239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8owk_17239/02_2025/8owk_17239.map" model { file = "/net/cci-nas-00/data/ceres_data/8owk_17239/02_2025/8owk_17239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8owk_17239/02_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-5592/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: 1.61, 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: 0.70 Conformation dependent library (CDL) restraints added in 352.5 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: 0.33 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: 0.68 Time building geometry restraints manager: 0.83 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: 0.660 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 11.060 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.770 ------------------------------------------------------------------------------- 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 : 0.308 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: 0.1586 time to fit residues: 27.9590 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 : 0.362 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.089528 restraints weight = 2270.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.090849 restraints weight = 1471.448| |-----------------------------------------------------------------------------| r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 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 : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 0 residues processed: 106 average time/residue: 0.1351 time to fit residues: 17.4682 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 : 0.351 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 3 optimal weight: 0.0070 chunk 23 optimal weight: 0.0570 chunk 17 optimal weight: 4.9990 overall best weight: 4.8122 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.097486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.078259 restraints weight = 5772.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.080357 restraints weight = 2312.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.081524 restraints weight = 1496.832| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3110 Z= 0.406 Angle : 0.752 8.357 4170 Z= 0.397 Chirality : 0.055 0.164 440 Planarity : 0.004 0.019 550 Dihedral : 5.910 16.984 410 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.58 % Allowed : 13.23 % Favored : 84.19 % 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: -2.28 (0.32), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.25), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS I 13 PHE 0.012 0.003 PHE I 4 TYR 0.015 0.003 TYR C 10 ARG 0.009 0.002 ARG D 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 79 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 GLN cc_start: 0.8267 (tt0) cc_final: 0.7746 (mt0) outliers start: 8 outliers final: 4 residues processed: 79 average time/residue: 0.1049 time to fit residues: 10.8231 Evaluate side-chains 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 0.0270 chunk 27 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 20.0000 chunk 20 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 0.3980 chunk 6 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.9442 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.097070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.077551 restraints weight = 5913.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.079600 restraints weight = 2359.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.080721 restraints weight = 1551.243| |-----------------------------------------------------------------------------| r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3110 Z= 0.328 Angle : 0.662 8.628 4170 Z= 0.343 Chirality : 0.053 0.127 440 Planarity : 0.003 0.017 550 Dihedral : 5.287 13.156 410 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.26 % Allowed : 11.94 % 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: -2.56 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS F 13 PHE 0.010 0.002 PHE H 20 TYR 0.012 0.002 TYR A 10 ARG 0.005 0.001 ARG D 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 80 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 80 average time/residue: 0.1015 time to fit residues: 10.5571 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 : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain E residue 6 HIS Chi-restraints excluded: chain F residue 6 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 6 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.095903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.076125 restraints weight = 5892.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.078031 restraints weight = 2393.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.079109 restraints weight = 1590.264| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 3110 Z= 0.339 Angle : 0.641 8.996 4170 Z= 0.336 Chirality : 0.052 0.133 440 Planarity : 0.003 0.022 550 Dihedral : 5.190 13.975 410 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.58 % Allowed : 13.23 % Favored : 84.19 % 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: -2.67 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS F 6 PHE 0.011 0.002 PHE F 4 TYR 0.011 0.002 TYR I 10 ARG 0.004 0.001 ARG D 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 80 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: B 3 GLU cc_start: 0.6553 (mp0) cc_final: 0.5630 (tm-30) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.0887 time to fit residues: 9.4599 Evaluate side-chains 76 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain E residue 6 HIS Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain J residue 6 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 20.0000 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.094261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.075011 restraints weight = 6260.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076845 restraints weight = 2525.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.077904 restraints weight = 1673.904| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 3110 Z= 0.388 Angle : 0.667 8.357 4170 Z= 0.356 Chirality : 0.053 0.147 440 Planarity : 0.003 0.021 550 Dihedral : 5.253 12.462 410 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.58 % Allowed : 13.87 % 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: -2.96 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS A 13 PHE 0.011 0.002 PHE F 19 TYR 0.010 0.002 TYR I 10 ARG 0.003 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 78 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.332 Fit side-chains REVERT: B 3 GLU cc_start: 0.6562 (mp0) cc_final: 0.5626 (tm-30) REVERT: G 3 GLU cc_start: 0.6618 (mp0) cc_final: 0.5640 (tm-30) outliers start: 8 outliers final: 5 residues processed: 78 average time/residue: 0.0937 time to fit residues: 9.7446 Evaluate side-chains 69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 64 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 H 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: 0.0570 chunk 19 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 11 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.1300 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.098569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.078556 restraints weight = 5727.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.080559 restraints weight = 2287.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.081717 restraints weight = 1514.628| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3110 Z= 0.161 Angle : 0.593 9.080 4170 Z= 0.300 Chirality : 0.051 0.143 440 Planarity : 0.002 0.009 550 Dihedral : 4.641 13.510 410 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % 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: -2.92 (0.31), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS E 6 PHE 0.020 0.001 PHE D 20 TYR 0.006 0.001 TYR I 10 ARG 0.003 0.000 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 79 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.346 Fit side-chains REVERT: B 3 GLU cc_start: 0.6682 (mp0) cc_final: 0.5889 (tm-30) REVERT: C 3 GLU cc_start: 0.6350 (mp0) cc_final: 0.5563 (tm-30) REVERT: E 5 ARG cc_start: 0.7330 (ttm110) cc_final: 0.6775 (tmm160) REVERT: G 3 GLU cc_start: 0.6718 (mp0) cc_final: 0.5892 (tm-30) REVERT: H 3 GLU cc_start: 0.6339 (mp0) cc_final: 0.5542 (tm-30) REVERT: J 5 ARG cc_start: 0.7470 (ttm110) cc_final: 0.6779 (tmm160) outliers start: 4 outliers final: 1 residues processed: 79 average time/residue: 0.1281 time to fit residues: 12.4703 Evaluate side-chains 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 20 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 20.0000 chunk 39 optimal weight: 0.0000 chunk 37 optimal weight: 7.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3818 r_free = 0.3818 target = 0.091887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.073154 restraints weight = 6271.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074907 restraints weight = 2554.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.075919 restraints weight = 1683.646| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 3110 Z= 0.479 Angle : 0.722 8.413 4170 Z= 0.396 Chirality : 0.054 0.153 440 Planarity : 0.004 0.027 550 Dihedral : 5.389 12.767 410 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % 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: -3.21 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.004 HIS E 13 PHE 0.013 0.003 PHE A 4 TYR 0.010 0.002 TYR C 10 ARG 0.014 0.002 ARG D 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 74 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 0.320 Fit side-chains REVERT: B 3 GLU cc_start: 0.6495 (mp0) cc_final: 0.5586 (tm-30) REVERT: G 3 GLU cc_start: 0.6524 (mp0) cc_final: 0.5577 (tm-30) outliers start: 4 outliers final: 2 residues processed: 74 average time/residue: 0.0821 time to fit residues: 8.3402 Evaluate side-chains 71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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: 20.0000 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 3 optimal weight: 0.0970 chunk 18 optimal weight: 6.9990 chunk 8 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- 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** J 6 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.096405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.076582 restraints weight = 5911.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.078487 restraints weight = 2386.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.079573 restraints weight = 1581.255| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3110 Z= 0.239 Angle : 0.627 8.243 4170 Z= 0.328 Chirality : 0.052 0.153 440 Planarity : 0.003 0.038 550 Dihedral : 4.773 12.249 410 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.65 % Allowed : 17.42 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.30), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.23), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS A 13 PHE 0.015 0.002 PHE J 4 TYR 0.007 0.002 TYR J 10 ARG 0.012 0.001 ARG D 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 75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.359 Fit side-chains REVERT: B 3 GLU cc_start: 0.6629 (mp0) cc_final: 0.5839 (tm-30) REVERT: C 3 GLU cc_start: 0.6357 (mp0) cc_final: 0.5704 (tm-30) REVERT: E 5 ARG cc_start: 0.7547 (ttm110) cc_final: 0.6869 (tmm160) REVERT: G 3 GLU cc_start: 0.6666 (mp0) cc_final: 0.5797 (tm-30) REVERT: G 5 ARG cc_start: 0.7216 (ttm110) cc_final: 0.6521 (tpm170) REVERT: H 3 GLU cc_start: 0.6357 (mp0) cc_final: 0.5655 (tm-30) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.1215 time to fit residues: 11.5356 Evaluate side-chains 70 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 2 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3813 r_free = 0.3813 target = 0.091219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.072304 restraints weight = 6195.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.073887 restraints weight = 2750.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.074731 restraints weight = 1886.681| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 3110 Z= 0.484 Angle : 0.732 8.145 4170 Z= 0.406 Chirality : 0.055 0.156 440 Planarity : 0.004 0.029 550 Dihedral : 5.405 12.785 410 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 0.97 % Allowed : 17.10 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (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 0.012 0.004 HIS I 13 PHE 0.013 0.003 PHE A 4 TYR 0.012 0.002 TYR J 10 ARG 0.013 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 75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.374 Fit side-chains REVERT: B 3 GLU cc_start: 0.6437 (mp0) cc_final: 0.5559 (tm-30) REVERT: E 5 ARG cc_start: 0.7791 (ttm110) cc_final: 0.6979 (tmm160) outliers start: 3 outliers final: 1 residues processed: 75 average time/residue: 0.0971 time to fit residues: 9.6462 Evaluate side-chains 71 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 29 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 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** ** 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 = 0.3875 r_free = 0.3875 target = 0.094177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.074548 restraints weight = 6096.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.076278 restraints weight = 2578.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.077190 restraints weight = 1736.594| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.6731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3110 Z= 0.297 Angle : 0.653 8.233 4170 Z= 0.349 Chirality : 0.054 0.152 440 Planarity : 0.003 0.034 550 Dihedral : 4.972 12.253 410 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.32 % Allowed : 18.39 % Favored : 81.29 % 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: -3.26 (0.29), residues: 380 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.22), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 13 PHE 0.015 0.002 PHE E 4 TYR 0.009 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: 1199.33 seconds wall clock time: 22 minutes 15.89 seconds (1335.89 seconds total)