Starting phenix.real_space_refine on Tue Aug 4 14:02:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vtw_65344/08_2026/9vtw_65344.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vtw_65344/08_2026/9vtw_65344.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vtw_65344/08_2026/9vtw_65344.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vtw_65344/08_2026/9vtw_65344.map" model { file = "/net/cci-nas-00/data/ceres_data/9vtw_65344/08_2026/9vtw_65344.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vtw_65344/08_2026/9vtw_65344.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 5 5.16 5 C 2325 2.51 5 N 590 2.21 5 O 675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3595 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain breaks: 1 Restraints were copied for chains: C, D, A, E Time building chain proxies: 0.67, per 1000 atoms: 0.19 Number of scatterers: 3595 At special positions: 0 Unit cell: (73.04, 82.17, 41.5, 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 5 16.00 O 675 8.00 N 590 7.00 C 2325 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: 0.16 Conformation dependent library (CDL) restraints added in 79.2 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 870 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 50.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 13 through 16 removed outlier: 6.352A pdb=" N VAL B 14 " --> pdb=" O LYS A 15 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL D 14 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21 removed outlier: 6.657A pdb=" N VAL B 20 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL D 20 " --> pdb=" O ARG E 21 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 25 through 27 removed outlier: 6.444A pdb=" N ALA B 25 " --> pdb=" O ILE C 26 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ALA D 25 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 30 through 34 removed outlier: 6.466A pdb=" N HIS B 31 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG C 34 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE B 33 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N HIS D 31 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG A 34 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N PHE D 33 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 59 through 66 removed outlier: 6.527A pdb=" N THR B 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLU C 63 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU B 62 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL C 65 " --> pdb=" O GLU B 62 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE B 64 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N PHE A 64 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 65 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU A 66 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR D 60 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N GLU A 63 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLU D 62 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL A 65 " --> pdb=" O GLU D 62 " (cutoff:3.500A) removed outlier: 9.142A pdb=" N PHE D 64 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE E 64 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL D 65 " --> pdb=" O PHE E 64 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLU E 66 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 71 through 73 removed outlier: 6.709A pdb=" N THR A 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL D 71 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ASP A 74 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ILE D 73 " --> pdb=" O ASP A 74 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N LYS A 76 " --> pdb=" O ILE D 73 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLU D 72 " --> pdb=" O ILE E 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 80 removed outlier: 6.989A pdb=" N LYS C 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N SER B 77 " --> pdb=" O LYS C 76 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR C 78 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 75 " --> pdb=" O ASP B 74 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER A 77 " --> pdb=" O LYS B 76 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TYR B 78 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER D 77 " --> pdb=" O LYS A 76 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 78 " --> pdb=" O SER D 77 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N LYS D 76 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 9.744A pdb=" N TRP E 79 " --> pdb=" O LYS D 76 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N TYR D 78 " --> pdb=" O TRP E 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 99 removed outlier: 6.382A pdb=" N GLU B 92 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE A 95 " --> pdb=" O GLU B 92 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL B 94 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N SER A 97 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR B 96 " --> pdb=" O SER A 97 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ASP A 99 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B 98 " --> pdb=" O ASP A 99 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N GLU D 92 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N PHE E 95 " --> pdb=" O GLU D 92 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL D 94 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N SER E 97 " --> pdb=" O VAL D 94 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR D 96 " --> pdb=" O SER E 97 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ASP E 99 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ASN D 98 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 104 through 110 removed outlier: 6.947A pdb=" N TYR C 105 " --> pdb=" O ARG B 104 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N THR B 106 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 107 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA B 108 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 9.194A pdb=" N TYR B 105 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N ALA A 108 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE B 107 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU A 110 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ALA B 109 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N TYR A 105 " --> pdb=" O ARG D 104 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR D 106 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE A 107 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA D 108 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N TYR D 105 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 10.070A pdb=" N ALA E 108 " --> pdb=" O TYR D 105 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE D 107 " --> pdb=" O ALA E 108 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N LEU E 110 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA D 109 " --> pdb=" O LEU E 110 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 114 through 115 removed outlier: 6.899A pdb=" N TYR B 114 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N TYR D 114 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 118 through 122 removed outlier: 5.954A pdb=" N THR B 118 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL C 121 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 120 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR D 118 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 121 " --> pdb=" O THR D 118 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA D 120 " --> pdb=" O VAL A 121 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 222 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: 0.57 Time building geometry restraints manager: 0.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1110 1.33 - 1.45: 496 1.45 - 1.56: 2064 1.56 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 3680 Sorted by residual: bond pdb=" CB VAL B 65 " pdb=" CG1 VAL B 65 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.41e+00 bond pdb=" CB VAL D 65 " pdb=" CG1 VAL D 65 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.41e+00 bond pdb=" CB VAL C 65 " pdb=" CG1 VAL C 65 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.40e+00 bond pdb=" CB VAL A 65 " pdb=" CG1 VAL A 65 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.40e+00 bond pdb=" CB VAL E 65 " pdb=" CG1 VAL E 65 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.39e+00 ... (remaining 3675 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 4728 1.59 - 3.19: 227 3.19 - 4.78: 40 4.78 - 6.38: 5 6.38 - 7.97: 5 Bond angle restraints: 5005 Sorted by residual: angle pdb=" CG1 VAL A 65 " pdb=" CB VAL A 65 " pdb=" CG2 VAL A 65 " ideal model delta sigma weight residual 110.80 102.83 7.97 2.20e+00 2.07e-01 1.31e+01 angle pdb=" CG1 VAL E 65 " pdb=" CB VAL E 65 " pdb=" CG2 VAL E 65 " ideal model delta sigma weight residual 110.80 102.84 7.96 2.20e+00 2.07e-01 1.31e+01 angle pdb=" CG1 VAL D 65 " pdb=" CB VAL D 65 " pdb=" CG2 VAL D 65 " ideal model delta sigma weight residual 110.80 102.85 7.95 2.20e+00 2.07e-01 1.31e+01 angle pdb=" CG1 VAL B 65 " pdb=" CB VAL B 65 " pdb=" CG2 VAL B 65 " ideal model delta sigma weight residual 110.80 102.85 7.95 2.20e+00 2.07e-01 1.30e+01 angle pdb=" CG1 VAL C 65 " pdb=" CB VAL C 65 " pdb=" CG2 VAL C 65 " ideal model delta sigma weight residual 110.80 102.86 7.94 2.20e+00 2.07e-01 1.30e+01 ... (remaining 5000 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.48: 1691 9.48 - 18.96: 314 18.96 - 28.43: 110 28.43 - 37.91: 35 37.91 - 47.39: 20 Dihedral angle restraints: 2170 sinusoidal: 825 harmonic: 1345 Sorted by residual: dihedral pdb=" CA ALA D 25 " pdb=" C ALA D 25 " pdb=" N ILE D 26 " pdb=" CA ILE D 26 " ideal model delta harmonic sigma weight residual 180.00 -164.67 -15.33 0 5.00e+00 4.00e-02 9.40e+00 dihedral pdb=" CA ALA C 25 " pdb=" C ALA C 25 " pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta harmonic sigma weight residual 180.00 -164.70 -15.30 0 5.00e+00 4.00e-02 9.37e+00 dihedral pdb=" CA ALA E 25 " pdb=" C ALA E 25 " pdb=" N ILE E 26 " pdb=" CA ILE E 26 " ideal model delta harmonic sigma weight residual -180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.36e+00 ... (remaining 2167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 225 0.027 - 0.053: 199 0.053 - 0.079: 67 0.079 - 0.106: 76 0.106 - 0.132: 23 Chirality restraints: 590 Sorted by residual: chirality pdb=" CA ILE E 73 " pdb=" N ILE E 73 " pdb=" C ILE E 73 " pdb=" CB ILE E 73 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 73 " pdb=" N ILE A 73 " pdb=" C ILE A 73 " pdb=" CB ILE A 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE C 73 " pdb=" N ILE C 73 " pdb=" C ILE C 73 " pdb=" CB ILE C 73 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 587 not shown) Planarity restraints: 615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 100 " 0.007 2.00e-02 2.50e+03 1.41e-02 2.00e+00 pdb=" C SER A 100 " -0.024 2.00e-02 2.50e+03 pdb=" O SER A 100 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY A 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 100 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C SER C 100 " -0.024 2.00e-02 2.50e+03 pdb=" O SER C 100 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 101 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 100 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.97e+00 pdb=" C SER B 100 " -0.024 2.00e-02 2.50e+03 pdb=" O SER B 100 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY B 101 " 0.008 2.00e-02 2.50e+03 ... (remaining 612 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 446 2.75 - 3.29: 3167 3.29 - 3.83: 5951 3.83 - 4.36: 7109 4.36 - 4.90: 13723 Nonbonded interactions: 30396 Sorted by model distance: nonbonded pdb=" OH TYR D 114 " pdb=" OG1 THR E 119 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR B 114 " pdb=" OG1 THR A 119 " model vdw 2.219 3.040 nonbonded pdb=" O SER E 100 " pdb=" OG SER E 100 " model vdw 2.236 3.040 nonbonded pdb=" O SER B 100 " pdb=" OG SER B 100 " model vdw 2.236 3.040 nonbonded pdb=" O SER A 100 " pdb=" OG SER A 100 " model vdw 2.236 3.040 ... (remaining 30391 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'A' selection = chain 'E' } 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 individual isotropic 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: 1.320 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 5.110 Find NCS groups from input model: 0.030 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:8.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 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 : 0.008 0.069 3680 Z= 0.363 Angle : 0.838 7.974 5005 Z= 0.486 Chirality : 0.052 0.132 590 Planarity : 0.004 0.030 615 Dihedral : 12.526 47.386 1300 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.04 (0.35), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 103 TYR 0.016 0.002 TYR D 114 PHE 0.008 0.002 PHE C 64 TRP 0.003 0.001 TRP C 79 HIS 0.002 0.001 HIS B 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00818 / 0.36 ( 3680) covalent geometry : angle 0.83821 / 0.49 ( 5005) hydrogen bonds : bond 0.15817 / 10.09 ( 69) hydrogen bonds : angle 8.83211 / 6.32 ( 222) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.085 Fit side-chains REVERT: B 21 ARG cc_start: 0.7664 (ttm170) cc_final: 0.7436 (ttt90) REVERT: B 85 SER cc_start: 0.7957 (t) cc_final: 0.7535 (p) REVERT: B 104 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7035 (mtm-85) REVERT: C 21 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7757 (ttt90) REVERT: C 89 GLU cc_start: 0.8287 (pt0) cc_final: 0.7853 (pt0) REVERT: C 104 ARG cc_start: 0.7839 (mtm180) cc_final: 0.6743 (mtm-85) REVERT: D 66 GLU cc_start: 0.8249 (tt0) cc_final: 0.7975 (tt0) REVERT: D 85 SER cc_start: 0.8015 (t) cc_final: 0.7645 (p) REVERT: D 104 ARG cc_start: 0.7840 (mtm180) cc_final: 0.6887 (mtm-85) REVERT: A 15 LYS cc_start: 0.8223 (mtmt) cc_final: 0.7812 (mtpt) REVERT: A 21 ARG cc_start: 0.7582 (ttm170) cc_final: 0.7340 (mtp-110) REVERT: A 66 GLU cc_start: 0.8341 (tt0) cc_final: 0.8084 (tt0) REVERT: A 85 SER cc_start: 0.8093 (t) cc_final: 0.7775 (p) REVERT: E 15 LYS cc_start: 0.8334 (mtmt) cc_final: 0.7384 (ttpt) REVERT: E 21 ARG cc_start: 0.7618 (ttm170) cc_final: 0.7314 (mtp-110) REVERT: E 66 GLU cc_start: 0.8343 (tt0) cc_final: 0.8141 (tt0) REVERT: E 85 SER cc_start: 0.8159 (t) cc_final: 0.7885 (p) REVERT: E 104 ARG cc_start: 0.8052 (mtm180) cc_final: 0.7151 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.8582 time to fit residues: 68.2455 Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** 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 = 0.3856 r_free = 0.3856 target = 0.126434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.104015 restraints weight = 4316.443| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.00 r_work: 0.3395 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3680 Z= 0.098 Angle : 0.515 4.346 5005 Z= 0.278 Chirality : 0.047 0.122 590 Planarity : 0.004 0.036 615 Dihedral : 4.690 14.910 495 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 12.91 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.71 (0.36), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 21 TYR 0.016 0.001 TYR A 114 PHE 0.008 0.002 PHE A 95 TRP 0.003 0.001 TRP C 79 HIS 0.001 0.000 HIS B 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 3680) covalent geometry : angle 0.51488 / 0.28 ( 5005) hydrogen bonds : bond 0.02436 / 1.41 ( 69) hydrogen bonds : angle 5.55640 / 3.96 ( 222) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.140 Fit side-chains REVERT: B 21 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7839 (mtp-110) REVERT: B 85 SER cc_start: 0.8160 (t) cc_final: 0.7913 (p) REVERT: B 89 GLU cc_start: 0.8428 (pt0) cc_final: 0.8217 (pt0) REVERT: B 104 ARG cc_start: 0.8448 (mtm180) cc_final: 0.7585 (mtm-85) REVERT: C 21 ARG cc_start: 0.8566 (ttm170) cc_final: 0.8162 (mtp-110) REVERT: C 89 GLU cc_start: 0.8557 (pt0) cc_final: 0.8218 (pt0) REVERT: C 104 ARG cc_start: 0.8407 (mtm180) cc_final: 0.7359 (mtt90) REVERT: D 21 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8056 (mtp-110) REVERT: D 66 GLU cc_start: 0.8588 (tt0) cc_final: 0.8356 (tt0) REVERT: D 85 SER cc_start: 0.8089 (t) cc_final: 0.7848 (p) REVERT: D 104 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7507 (mtm-85) REVERT: A 15 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8382 (mtpt) REVERT: A 21 ARG cc_start: 0.8293 (ttm170) cc_final: 0.7836 (mtp-110) REVERT: A 76 LYS cc_start: 0.8265 (mmtt) cc_final: 0.7958 (mptt) REVERT: A 85 SER cc_start: 0.8080 (t) cc_final: 0.7750 (p) REVERT: A 99 ASP cc_start: 0.7873 (t0) cc_final: 0.7654 (t0) REVERT: E 21 ARG cc_start: 0.8258 (ttm170) cc_final: 0.7698 (mtp-110) REVERT: E 76 LYS cc_start: 0.7902 (mmtt) cc_final: 0.7645 (mmtt) REVERT: E 85 SER cc_start: 0.8311 (t) cc_final: 0.8031 (p) REVERT: E 104 ARG cc_start: 0.8553 (mtm180) cc_final: 0.7532 (mtt-85) outliers start: 6 outliers final: 3 residues processed: 70 average time/residue: 0.8340 time to fit residues: 59.5577 Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 29 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3756 r_free = 0.3756 target = 0.118148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.094679 restraints weight = 4294.305| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.07 r_work: 0.3251 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9115 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3680 Z= 0.288 Angle : 0.658 4.543 5005 Z= 0.353 Chirality : 0.051 0.139 590 Planarity : 0.004 0.034 615 Dihedral : 5.099 15.383 495 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.04 % Allowed : 13.42 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 21 TYR 0.020 0.002 TYR B 114 PHE 0.020 0.003 PHE A 33 TRP 0.004 0.001 TRP A 79 HIS 0.002 0.001 HIS D 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00703 / 0.29 ( 3680) covalent geometry : angle 0.65800 / 0.35 ( 5005) hydrogen bonds : bond 0.02750 / 1.71 ( 69) hydrogen bonds : angle 5.24205 / 3.75 ( 222) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.136 Fit side-chains REVERT: B 21 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7864 (mtp-110) REVERT: B 62 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8040 (mt-10) REVERT: B 85 SER cc_start: 0.8314 (t) cc_final: 0.7950 (p) REVERT: B 89 GLU cc_start: 0.8488 (pt0) cc_final: 0.8287 (pt0) REVERT: B 104 ARG cc_start: 0.8403 (mtm180) cc_final: 0.7401 (mtm-85) REVERT: C 21 ARG cc_start: 0.8579 (ttm170) cc_final: 0.8100 (ttt90) REVERT: C 89 GLU cc_start: 0.8565 (pt0) cc_final: 0.8218 (pt0) REVERT: C 104 ARG cc_start: 0.8469 (mtm180) cc_final: 0.7334 (mtm-85) REVERT: D 66 GLU cc_start: 0.8566 (tt0) cc_final: 0.8355 (tt0) REVERT: D 85 SER cc_start: 0.8132 (t) cc_final: 0.7818 (p) REVERT: D 104 ARG cc_start: 0.8470 (mtm180) cc_final: 0.7414 (mtt-85) REVERT: A 15 LYS cc_start: 0.8747 (mtmt) cc_final: 0.8481 (mtpt) REVERT: A 21 ARG cc_start: 0.8295 (ttm170) cc_final: 0.7781 (ttt90) REVERT: A 76 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7965 (mptt) REVERT: A 85 SER cc_start: 0.8237 (t) cc_final: 0.7835 (p) REVERT: A 104 ARG cc_start: 0.8553 (mtm180) cc_final: 0.7555 (mtm-85) REVERT: E 15 LYS cc_start: 0.8602 (mtpt) cc_final: 0.7969 (ttpt) REVERT: E 21 ARG cc_start: 0.8296 (ttm170) cc_final: 0.7821 (mtp-110) REVERT: E 85 SER cc_start: 0.8431 (t) cc_final: 0.8195 (p) REVERT: E 104 ARG cc_start: 0.8666 (mtm180) cc_final: 0.7597 (mtt-85) outliers start: 12 outliers final: 10 residues processed: 68 average time/residue: 0.7781 time to fit residues: 53.9978 Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 89 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 0.0570 chunk 41 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.129358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.107885 restraints weight = 4151.861| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.00 r_work: 0.3456 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8991 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 3680 Z= 0.082 Angle : 0.475 3.969 5005 Z= 0.256 Chirality : 0.047 0.122 590 Planarity : 0.003 0.030 615 Dihedral : 4.444 14.786 495 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.03 % Allowed : 15.95 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 34 TYR 0.014 0.001 TYR A 114 PHE 0.008 0.001 PHE A 64 TRP 0.002 0.000 TRP A 79 HIS 0.001 0.000 HIS A 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.08 ( 3680) covalent geometry : angle 0.47470 / 0.26 ( 5005) hydrogen bonds : bond 0.01752 / 1.00 ( 69) hydrogen bonds : angle 4.87008 / 3.45 ( 222) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.166 Fit side-chains REVERT: B 15 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7700 (ttpt) REVERT: B 21 ARG cc_start: 0.8140 (ttm170) cc_final: 0.7778 (mtp-110) REVERT: B 85 SER cc_start: 0.8202 (t) cc_final: 0.7962 (p) REVERT: B 89 GLU cc_start: 0.8363 (pt0) cc_final: 0.8154 (pt0) REVERT: B 104 ARG cc_start: 0.8403 (mtm180) cc_final: 0.7445 (mtm-85) REVERT: C 21 ARG cc_start: 0.8487 (ttm170) cc_final: 0.8111 (mtp-110) REVERT: C 89 GLU cc_start: 0.8481 (pt0) cc_final: 0.8174 (pt0) REVERT: C 104 ARG cc_start: 0.8400 (mtm180) cc_final: 0.7311 (mtt90) REVERT: D 21 ARG cc_start: 0.8182 (ttt180) cc_final: 0.7893 (mtp-110) REVERT: D 66 GLU cc_start: 0.8491 (tt0) cc_final: 0.8274 (tt0) REVERT: D 85 SER cc_start: 0.7941 (t) cc_final: 0.7585 (p) REVERT: D 104 ARG cc_start: 0.8414 (mtm180) cc_final: 0.7424 (mtm-85) REVERT: A 15 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8143 (mtpt) REVERT: A 21 ARG cc_start: 0.8207 (ttm170) cc_final: 0.7789 (mtp-110) REVERT: A 85 SER cc_start: 0.8109 (t) cc_final: 0.7717 (p) REVERT: A 104 ARG cc_start: 0.8425 (mtm180) cc_final: 0.7357 (mtm-85) REVERT: E 15 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8156 (ttpt) REVERT: E 21 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7700 (mtp-110) REVERT: E 76 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7615 (mmtt) REVERT: E 85 SER cc_start: 0.8213 (t) cc_final: 0.7892 (p) REVERT: E 104 ARG cc_start: 0.8490 (mtm180) cc_final: 0.7633 (mtt-85) outliers start: 8 outliers final: 5 residues processed: 76 average time/residue: 0.7703 time to fit residues: 59.7779 Evaluate side-chains 70 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 65 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.121083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097915 restraints weight = 4162.356| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.11 r_work: 0.3339 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 3680 Z= 0.152 Angle : 0.530 4.059 5005 Z= 0.286 Chirality : 0.048 0.132 590 Planarity : 0.003 0.027 615 Dihedral : 4.651 14.495 495 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.04 % Allowed : 16.46 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.38), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 104 TYR 0.016 0.002 TYR A 114 PHE 0.011 0.002 PHE A 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 ( 3680) covalent geometry : angle 0.53028 / 0.29 ( 5005) hydrogen bonds : bond 0.01998 / 1.22 ( 69) hydrogen bonds : angle 4.83610 / 3.44 ( 222) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.140 Fit side-chains REVERT: B 15 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7624 (ttpt) REVERT: B 21 ARG cc_start: 0.8194 (ttm170) cc_final: 0.7769 (mtp-110) REVERT: B 85 SER cc_start: 0.8215 (t) cc_final: 0.7965 (p) REVERT: B 89 GLU cc_start: 0.8438 (pt0) cc_final: 0.8217 (pt0) REVERT: B 99 ASP cc_start: 0.8289 (t0) cc_final: 0.8080 (t0) REVERT: B 104 ARG cc_start: 0.8375 (mtm180) cc_final: 0.7375 (mtm-85) REVERT: C 15 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8198 (ttpt) REVERT: C 21 ARG cc_start: 0.8525 (ttm170) cc_final: 0.8111 (mtp-110) REVERT: C 89 GLU cc_start: 0.8518 (pt0) cc_final: 0.8187 (pt0) REVERT: C 104 ARG cc_start: 0.8416 (mtm180) cc_final: 0.7318 (mtm-85) REVERT: D 66 GLU cc_start: 0.8556 (tt0) cc_final: 0.8303 (tt0) REVERT: D 85 SER cc_start: 0.8007 (t) cc_final: 0.7750 (p) REVERT: D 104 ARG cc_start: 0.8430 (mtm180) cc_final: 0.7402 (mtm-85) REVERT: A 15 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8308 (mtpt) REVERT: A 21 ARG cc_start: 0.8284 (ttm170) cc_final: 0.7810 (mtp-110) REVERT: A 85 SER cc_start: 0.8135 (t) cc_final: 0.7733 (p) REVERT: A 104 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7473 (mtm-85) REVERT: E 15 LYS cc_start: 0.8574 (mtpt) cc_final: 0.8003 (ttpt) REVERT: E 21 ARG cc_start: 0.8192 (ttm170) cc_final: 0.7712 (mtp-110) REVERT: E 76 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7122 (mttt) REVERT: E 85 SER cc_start: 0.8271 (t) cc_final: 0.8017 (p) REVERT: E 104 ARG cc_start: 0.8670 (mtm180) cc_final: 0.7656 (mtt-85) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.8905 time to fit residues: 62.6497 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3772 r_free = 0.3772 target = 0.118822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095599 restraints weight = 4322.011| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.08 r_work: 0.3275 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3680 Z= 0.206 Angle : 0.576 4.179 5005 Z= 0.312 Chirality : 0.049 0.134 590 Planarity : 0.004 0.028 615 Dihedral : 4.864 14.522 495 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.80 % Allowed : 16.46 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.38), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.017 0.002 TYR B 114 PHE 0.014 0.003 PHE A 33 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 ( 3680) covalent geometry : angle 0.57636 / 0.31 ( 5005) hydrogen bonds : bond 0.02214 / 1.37 ( 69) hydrogen bonds : angle 4.91007 / 3.52 ( 222) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.093 Fit side-chains REVERT: B 21 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7819 (mtp-110) REVERT: B 62 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8108 (mt-10) REVERT: B 63 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: B 85 SER cc_start: 0.8306 (t) cc_final: 0.7986 (p) REVERT: B 99 ASP cc_start: 0.8353 (t0) cc_final: 0.8068 (t0) REVERT: B 104 ARG cc_start: 0.8394 (mtm180) cc_final: 0.7441 (mtm-85) REVERT: C 21 ARG cc_start: 0.8599 (ttm170) cc_final: 0.8165 (mtp-110) REVERT: C 89 GLU cc_start: 0.8505 (pt0) cc_final: 0.8204 (pt0) REVERT: C 104 ARG cc_start: 0.8492 (mtm180) cc_final: 0.7400 (mtm-85) REVERT: D 66 GLU cc_start: 0.8589 (tt0) cc_final: 0.8383 (tt0) REVERT: D 85 SER cc_start: 0.8083 (t) cc_final: 0.7747 (p) REVERT: D 104 ARG cc_start: 0.8466 (mtm180) cc_final: 0.7389 (mtm-85) REVERT: A 15 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8484 (mtpt) REVERT: A 21 ARG cc_start: 0.8346 (ttm170) cc_final: 0.7870 (mtp-110) REVERT: A 85 SER cc_start: 0.8237 (t) cc_final: 0.7801 (p) REVERT: A 104 ARG cc_start: 0.8562 (mtm180) cc_final: 0.7584 (mtm-85) REVERT: E 21 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7806 (mtp-110) REVERT: E 70 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8615 (ttmt) REVERT: E 76 LYS cc_start: 0.7755 (mmtt) cc_final: 0.7190 (mttp) REVERT: E 85 SER cc_start: 0.8374 (t) cc_final: 0.8137 (p) REVERT: E 104 ARG cc_start: 0.8734 (mtm180) cc_final: 0.7698 (mtt-85) outliers start: 15 outliers final: 9 residues processed: 68 average time/residue: 0.8256 time to fit residues: 57.3569 Evaluate side-chains 69 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 70 LYS Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3739 r_free = 0.3739 target = 0.116369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.093163 restraints weight = 4454.743| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.10 r_work: 0.3249 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3680 Z= 0.236 Angle : 0.601 4.235 5005 Z= 0.326 Chirality : 0.050 0.134 590 Planarity : 0.004 0.028 615 Dihedral : 4.975 14.722 495 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.80 % Allowed : 16.46 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 104 TYR 0.018 0.002 TYR B 114 PHE 0.016 0.003 PHE A 33 TRP 0.004 0.001 TRP E 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 ( 3680) covalent geometry : angle 0.60094 / 0.33 ( 5005) hydrogen bonds : bond 0.02319 / 1.44 ( 69) hydrogen bonds : angle 4.96454 / 3.56 ( 222) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.083 Fit side-chains REVERT: B 15 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7862 (ttpt) REVERT: B 21 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7789 (mtp-110) REVERT: B 62 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 85 SER cc_start: 0.8306 (t) cc_final: 0.8004 (p) REVERT: B 99 ASP cc_start: 0.8384 (t0) cc_final: 0.8144 (t0) REVERT: B 104 ARG cc_start: 0.8387 (mtm180) cc_final: 0.7397 (mtm-85) REVERT: C 21 ARG cc_start: 0.8613 (ttm170) cc_final: 0.8171 (mtp-110) REVERT: C 89 GLU cc_start: 0.8434 (pt0) cc_final: 0.8231 (pt0) REVERT: C 104 ARG cc_start: 0.8503 (mtm180) cc_final: 0.7384 (mtm-85) REVERT: D 66 GLU cc_start: 0.8586 (tt0) cc_final: 0.8385 (tt0) REVERT: D 104 ARG cc_start: 0.8459 (mtm180) cc_final: 0.7337 (mtm-85) REVERT: A 21 ARG cc_start: 0.8337 (ttm170) cc_final: 0.7852 (mtp-110) REVERT: A 85 SER cc_start: 0.8181 (t) cc_final: 0.7753 (p) REVERT: A 104 ARG cc_start: 0.8569 (mtm180) cc_final: 0.7554 (mtm-85) REVERT: E 21 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7793 (mtp-110) REVERT: E 76 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7123 (mttt) REVERT: E 85 SER cc_start: 0.8382 (t) cc_final: 0.8182 (p) REVERT: E 104 ARG cc_start: 0.8747 (mtm180) cc_final: 0.7696 (mtt-85) outliers start: 15 outliers final: 13 residues processed: 68 average time/residue: 0.7603 time to fit residues: 52.7654 Evaluate side-chains 68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 55 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3778 r_free = 0.3778 target = 0.120899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098140 restraints weight = 4375.397| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.16 r_work: 0.3331 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9038 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3680 Z= 0.131 Angle : 0.518 3.907 5005 Z= 0.281 Chirality : 0.048 0.128 590 Planarity : 0.004 0.027 615 Dihedral : 4.711 14.601 495 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.29 % Allowed : 17.22 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.015 0.001 TYR A 114 PHE 0.009 0.002 PHE A 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 3680) covalent geometry : angle 0.51841 / 0.28 ( 5005) hydrogen bonds : bond 0.01910 / 1.15 ( 69) hydrogen bonds : angle 4.81594 / 3.44 ( 222) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.132 Fit side-chains REVERT: B 15 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7748 (ttpt) REVERT: B 21 ARG cc_start: 0.8212 (ttm170) cc_final: 0.7759 (mtp-110) REVERT: B 62 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 85 SER cc_start: 0.8258 (t) cc_final: 0.7955 (p) REVERT: B 99 ASP cc_start: 0.8290 (t0) cc_final: 0.8021 (t70) REVERT: B 104 ARG cc_start: 0.8348 (mtm180) cc_final: 0.7317 (mtm-85) REVERT: C 21 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8141 (mtp-110) REVERT: C 89 GLU cc_start: 0.8399 (pt0) cc_final: 0.8091 (pt0) REVERT: C 104 ARG cc_start: 0.8428 (mtm180) cc_final: 0.7325 (mtt90) REVERT: D 66 GLU cc_start: 0.8558 (tt0) cc_final: 0.8319 (tt0) REVERT: D 104 ARG cc_start: 0.8401 (mtm180) cc_final: 0.7296 (mtm-85) REVERT: A 15 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8256 (mtpt) REVERT: A 21 ARG cc_start: 0.8232 (ttm170) cc_final: 0.7792 (mtp-110) REVERT: A 85 SER cc_start: 0.8188 (t) cc_final: 0.7734 (p) REVERT: A 104 ARG cc_start: 0.8440 (mtm180) cc_final: 0.7415 (mtm-85) REVERT: E 15 LYS cc_start: 0.8510 (mtpt) cc_final: 0.7924 (ttpt) REVERT: E 21 ARG cc_start: 0.8173 (ttm170) cc_final: 0.7694 (mtp-110) REVERT: E 76 LYS cc_start: 0.7694 (mmtt) cc_final: 0.7103 (mttt) REVERT: E 85 SER cc_start: 0.8241 (t) cc_final: 0.7981 (p) REVERT: E 104 ARG cc_start: 0.8711 (mtm180) cc_final: 0.7645 (mtt-85) outliers start: 13 outliers final: 9 residues processed: 63 average time/residue: 0.8225 time to fit residues: 52.8753 Evaluate side-chains 62 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 97 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3770 r_free = 0.3770 target = 0.119475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.096119 restraints weight = 4268.853| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.04 r_work: 0.3262 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9120 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 3680 Z= 0.242 Angle : 0.606 4.187 5005 Z= 0.328 Chirality : 0.050 0.127 590 Planarity : 0.004 0.026 615 Dihedral : 4.980 14.613 495 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.05 % Allowed : 16.46 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 104 TYR 0.018 0.002 TYR B 114 PHE 0.016 0.003 PHE A 33 TRP 0.003 0.001 TRP E 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.24 ( 3680) covalent geometry : angle 0.60630 / 0.33 ( 5005) hydrogen bonds : bond 0.02314 / 1.44 ( 69) hydrogen bonds : angle 4.95225 / 3.55 ( 222) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.084 Fit side-chains REVERT: B 15 LYS cc_start: 0.8450 (mtpt) cc_final: 0.7931 (ttpt) REVERT: B 21 ARG cc_start: 0.8289 (ttm170) cc_final: 0.7853 (mtp-110) REVERT: B 62 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8138 (mt-10) REVERT: B 85 SER cc_start: 0.8370 (t) cc_final: 0.8015 (p) REVERT: B 99 ASP cc_start: 0.8371 (t0) cc_final: 0.8131 (t70) REVERT: B 104 ARG cc_start: 0.8412 (mtm180) cc_final: 0.7465 (mtm-85) REVERT: C 21 ARG cc_start: 0.8613 (ttm170) cc_final: 0.8181 (mtp-110) REVERT: C 89 GLU cc_start: 0.8446 (pt0) cc_final: 0.8240 (pt0) REVERT: C 104 ARG cc_start: 0.8504 (mtm180) cc_final: 0.7433 (mtm-85) REVERT: D 104 ARG cc_start: 0.8482 (mtm180) cc_final: 0.7388 (mtm-85) REVERT: A 15 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8407 (mtpt) REVERT: A 21 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7901 (mtp-110) REVERT: A 85 SER cc_start: 0.8241 (t) cc_final: 0.7820 (p) REVERT: A 104 ARG cc_start: 0.8592 (mtm180) cc_final: 0.7608 (mtm-85) REVERT: E 15 LYS cc_start: 0.8613 (mtpt) cc_final: 0.7932 (ttpt) REVERT: E 21 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7832 (mtp-110) REVERT: E 76 LYS cc_start: 0.7760 (mmtt) cc_final: 0.7188 (mttt) REVERT: E 85 SER cc_start: 0.8396 (t) cc_final: 0.8171 (p) REVERT: E 104 ARG cc_start: 0.8757 (mtm180) cc_final: 0.7729 (mtt-85) outliers start: 16 outliers final: 12 residues processed: 67 average time/residue: 0.7046 time to fit residues: 48.2389 Evaluate side-chains 68 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** 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 = 0.3808 r_free = 0.3808 target = 0.122426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.099080 restraints weight = 4350.207| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.06 r_work: 0.3301 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9107 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3680 Z= 0.181 Angle : 0.560 4.037 5005 Z= 0.303 Chirality : 0.048 0.125 590 Planarity : 0.004 0.026 615 Dihedral : 4.890 14.717 495 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.78 % Allowed : 18.23 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.37), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 34 TYR 0.017 0.002 TYR A 114 PHE 0.013 0.002 PHE A 33 TRP 0.002 0.001 TRP C 79 HIS 0.002 0.001 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 ( 3680) covalent geometry : angle 0.56037 / 0.30 ( 5005) hydrogen bonds : bond 0.02102 / 1.28 ( 69) hydrogen bonds : angle 4.88123 / 3.49 ( 222) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.149 Fit side-chains REVERT: B 15 LYS cc_start: 0.8432 (mtpt) cc_final: 0.7916 (ttpt) REVERT: B 21 ARG cc_start: 0.8264 (ttm170) cc_final: 0.7846 (mtp-110) REVERT: B 62 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8120 (mt-10) REVERT: B 85 SER cc_start: 0.8339 (t) cc_final: 0.8015 (p) REVERT: B 104 ARG cc_start: 0.8432 (mtm180) cc_final: 0.7496 (mtm-85) REVERT: C 21 ARG cc_start: 0.8591 (ttm170) cc_final: 0.8188 (mtp-110) REVERT: C 89 GLU cc_start: 0.8451 (pt0) cc_final: 0.8249 (pt0) REVERT: C 104 ARG cc_start: 0.8513 (mtm180) cc_final: 0.7432 (mtm-85) REVERT: D 104 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7380 (mtm-85) REVERT: A 15 LYS cc_start: 0.8697 (mtmt) cc_final: 0.8390 (mtpt) REVERT: A 21 ARG cc_start: 0.8302 (ttm170) cc_final: 0.7896 (mtp-110) REVERT: A 85 SER cc_start: 0.8205 (t) cc_final: 0.7787 (p) REVERT: A 104 ARG cc_start: 0.8565 (mtm180) cc_final: 0.7607 (mtm-85) REVERT: E 15 LYS cc_start: 0.8582 (mtpt) cc_final: 0.7935 (ttpt) REVERT: E 21 ARG cc_start: 0.8275 (ttm170) cc_final: 0.7821 (mtp-110) REVERT: E 76 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7206 (mttt) REVERT: E 85 SER cc_start: 0.8335 (t) cc_final: 0.8131 (p) REVERT: E 104 ARG cc_start: 0.8757 (mtm180) cc_final: 0.7719 (mtt-85) outliers start: 11 outliers final: 11 residues processed: 63 average time/residue: 0.6253 time to fit residues: 40.1885 Evaluate side-chains 66 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain C residue 66 GLU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 89 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 9 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.120373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.097757 restraints weight = 4282.410| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.10 r_work: 0.3331 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3680 Z= 0.135 Angle : 0.521 3.930 5005 Z= 0.283 Chirality : 0.047 0.124 590 Planarity : 0.003 0.026 615 Dihedral : 4.735 14.609 495 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.29 % Allowed : 17.72 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.38), residues: 440 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 103 TYR 0.016 0.002 TYR A 114 PHE 0.009 0.002 PHE A 33 TRP 0.002 0.001 TRP A 79 HIS 0.002 0.000 HIS A 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 3680) covalent geometry : angle 0.52130 / 0.28 ( 5005) hydrogen bonds : bond 0.01916 / 1.15 ( 69) hydrogen bonds : angle 4.80164 / 3.43 ( 222) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.02 seconds wall clock time: 26 minutes 48.58 seconds (1608.58 seconds total)