Starting phenix.real_space_refine on Wed Jul 1 23:00:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf7_29980/07_2026/8gf7_29980.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 2346 2.51 5 N 654 2.21 5 O 774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3774 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 615 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 0.79, per 1000 atoms: 0.21 Number of scatterers: 3774 At special positions: 0 Unit cell: (103.2, 116.1, 32.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 774 8.00 N 654 7.00 C 2346 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=6, symmetry=0 Links applied NAG-SER " NAG A 101 " - " SER A 87 " " NAG B 101 " - " SER B 87 " " NAG C 101 " - " SER C 87 " " NAG D 101 " - " SER D 87 " " NAG E 101 " - " SER E 87 " " NAG F 101 " - " SER F 87 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 161.2 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 8 through 9 removed outlier: 6.538A pdb=" N LEU A 8 " --> pdb=" O SER C 9 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 13 through 23 removed outlier: 8.203A pdb=" N GLY A 14 " --> pdb=" O VAL B 15 " (cutoff:3.500A) removed outlier: 10.576A pdb=" N ALA B 17 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL A 16 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N ALA B 19 " --> pdb=" O VAL A 16 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 18 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N LYS B 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLU A 20 " --> pdb=" O LYS B 21 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N LYS B 23 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR A 22 " --> pdb=" O LYS B 23 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 14 " --> pdb=" O GLU C 13 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA A 18 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA C 19 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU A 20 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS C 21 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 22 " --> pdb=" O LYS C 21 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LYS C 23 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 31 removed outlier: 6.856A pdb=" N ALA A 27 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU B 28 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA A 29 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ALA B 30 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N VAL A 26 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 10.665A pdb=" N ALA C 29 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N GLU A 28 " --> pdb=" O ALA C 29 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N GLY C 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ALA A 30 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 43 removed outlier: 6.339A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 48 through 49 removed outlier: 6.628A pdb=" N VAL A 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 54 removed outlier: 6.691A pdb=" N VAL A 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 60 through 66 removed outlier: 6.833A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N VAL C 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ASN C 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 70 through 77 removed outlier: 7.094A pdb=" N VAL B 74 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA B 76 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL A 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N GLY C 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N THR A 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR C 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 10.462A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.730A pdb=" N LYS A 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 85 through 86 removed outlier: 7.059A pdb=" N ALA A 85 " --> pdb=" O GLY B 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 89 through 90 removed outlier: 6.660A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 93 through 95 removed outlier: 6.221A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 8 through 9 Processing sheet with id=AB5, first strand: chain 'D' and resid 13 through 23 removed outlier: 8.125A pdb=" N GLY D 14 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 10.515A pdb=" N ALA E 17 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL D 16 " --> pdb=" O ALA E 17 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ALA E 19 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA D 18 " --> pdb=" O ALA E 19 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LYS E 21 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLU D 20 " --> pdb=" O LYS E 21 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LYS E 23 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR D 22 " --> pdb=" O LYS E 23 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N GLY E 14 " --> pdb=" O VAL F 15 " (cutoff:3.500A) removed outlier: 10.516A pdb=" N ALA F 17 " --> pdb=" O GLY E 14 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL E 16 " --> pdb=" O ALA F 17 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ALA F 19 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA E 18 " --> pdb=" O ALA F 19 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N LYS F 21 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU E 20 " --> pdb=" O LYS F 21 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N LYS F 23 " --> pdb=" O GLU E 20 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR E 22 " --> pdb=" O LYS F 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 26 through 31 removed outlier: 6.840A pdb=" N ALA D 27 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU E 28 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA D 29 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA E 30 " --> pdb=" O ALA D 29 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ALA E 27 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLU F 28 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALA E 29 " --> pdb=" O GLU F 28 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA F 30 " --> pdb=" O ALA E 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 38 through 43 removed outlier: 6.256A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N TYR E 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N SER F 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLY E 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 48 through 49 Processing sheet with id=AB9, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AC1, first strand: chain 'D' and resid 60 through 66 Processing sheet with id=AC2, first strand: chain 'D' and resid 70 through 77 removed outlier: 7.072A pdb=" N VAL E 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR D 75 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA E 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL D 77 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL F 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N THR E 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA F 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL E 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 80 through 81 removed outlier: 6.672A pdb=" N LYS D 80 " --> pdb=" O THR E 81 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS E 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 85 through 86 removed outlier: 7.083A pdb=" N ALA D 85 " --> pdb=" O GLY E 86 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ALA E 85 " --> pdb=" O GLY F 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 89 through 90 removed outlier: 6.684A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA E 89 " --> pdb=" O ALA F 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'D' and resid 93 through 95 removed outlier: 6.254A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE E 94 " --> pdb=" O VAL F 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 49 hydrogen bonds defined for protein. 147 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: 0.52 Time building geometry restraints manager: 0.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 666 1.28 - 1.35: 576 1.35 - 1.42: 102 1.42 - 1.49: 648 1.49 - 1.55: 1794 Bond restraints: 3786 Sorted by residual: bond pdb=" C3 NAG E 101 " pdb=" O3 NAG E 101 " ideal model delta sigma weight residual 1.403 1.430 -0.027 2.00e-02 2.50e+03 1.79e+00 bond pdb=" C2 NAG F 101 " pdb=" N2 NAG F 101 " ideal model delta sigma weight residual 1.439 1.465 -0.026 2.00e-02 2.50e+03 1.72e+00 bond pdb=" C3 NAG F 101 " pdb=" O3 NAG F 101 " ideal model delta sigma weight residual 1.403 1.429 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C3 NAG B 101 " pdb=" O3 NAG B 101 " ideal model delta sigma weight residual 1.403 1.429 -0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" C3 NAG A 101 " pdb=" O3 NAG A 101 " ideal model delta sigma weight residual 1.403 1.429 -0.026 2.00e-02 2.50e+03 1.68e+00 ... (remaining 3781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 4633 0.99 - 1.99: 344 1.99 - 2.98: 81 2.98 - 3.98: 18 3.98 - 4.97: 18 Bond angle restraints: 5094 Sorted by residual: angle pdb=" C ALA C 11 " pdb=" N LYS C 12 " pdb=" CA LYS C 12 " ideal model delta sigma weight residual 122.56 118.91 3.65 1.50e+00 4.44e-01 5.93e+00 angle pdb=" C ALA F 11 " pdb=" N LYS F 12 " pdb=" CA LYS F 12 " ideal model delta sigma weight residual 122.56 118.92 3.64 1.50e+00 4.44e-01 5.90e+00 angle pdb=" C ALA D 11 " pdb=" N LYS D 12 " pdb=" CA LYS D 12 " ideal model delta sigma weight residual 122.56 118.92 3.64 1.50e+00 4.44e-01 5.88e+00 angle pdb=" C ALA B 11 " pdb=" N LYS B 12 " pdb=" CA LYS B 12 " ideal model delta sigma weight residual 122.56 118.93 3.63 1.50e+00 4.44e-01 5.87e+00 angle pdb=" C ALA A 11 " pdb=" N LYS A 12 " pdb=" CA LYS A 12 " ideal model delta sigma weight residual 122.56 118.94 3.62 1.50e+00 4.44e-01 5.82e+00 ... (remaining 5089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.15: 1962 10.15 - 20.30: 162 20.30 - 30.44: 60 30.44 - 40.59: 12 40.59 - 50.74: 6 Dihedral angle restraints: 2202 sinusoidal: 750 harmonic: 1452 Sorted by residual: dihedral pdb=" CA LYS D 32 " pdb=" C LYS D 32 " pdb=" N THR D 33 " pdb=" CA THR D 33 " ideal model delta harmonic sigma weight residual 180.00 160.97 19.03 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA LYS A 32 " pdb=" C LYS A 32 " pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA LYS C 32 " pdb=" C LYS C 32 " pdb=" N THR C 33 " pdb=" CA THR C 33 " ideal model delta harmonic sigma weight residual 180.00 161.00 19.00 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 2199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 423 0.035 - 0.071: 87 0.071 - 0.106: 84 0.106 - 0.142: 48 0.142 - 0.177: 18 Chirality restraints: 660 Sorted by residual: chirality pdb=" C5 NAG F 101 " pdb=" C4 NAG F 101 " pdb=" C6 NAG F 101 " pdb=" O5 NAG F 101 " both_signs ideal model delta sigma weight residual False -2.41 -2.59 0.18 2.00e-01 2.50e+01 7.83e-01 chirality pdb=" C5 NAG B 101 " pdb=" C4 NAG B 101 " pdb=" C6 NAG B 101 " pdb=" O5 NAG B 101 " both_signs ideal model delta sigma weight residual False -2.41 -2.58 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" C5 NAG A 101 " pdb=" C4 NAG A 101 " pdb=" C6 NAG A 101 " pdb=" O5 NAG A 101 " both_signs ideal model delta sigma weight residual False -2.41 -2.58 0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 657 not shown) Planarity restraints: 630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 15 " -0.002 2.00e-02 2.50e+03 4.18e-03 1.75e-01 pdb=" C VAL F 15 " 0.007 2.00e-02 2.50e+03 pdb=" O VAL F 15 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL F 16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 15 " -0.002 2.00e-02 2.50e+03 4.11e-03 1.69e-01 pdb=" C VAL D 15 " 0.007 2.00e-02 2.50e+03 pdb=" O VAL D 15 " -0.003 2.00e-02 2.50e+03 pdb=" N VAL D 16 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 59 " 0.002 2.00e-02 2.50e+03 4.05e-03 1.64e-01 pdb=" C THR E 59 " -0.007 2.00e-02 2.50e+03 pdb=" O THR E 59 " 0.003 2.00e-02 2.50e+03 pdb=" N LYS E 60 " 0.002 2.00e-02 2.50e+03 ... (remaining 627 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 35 2.32 - 2.97: 1747 2.97 - 3.61: 5076 3.61 - 4.26: 7164 4.26 - 4.90: 11983 Nonbonded interactions: 26005 Sorted by model distance: nonbonded pdb=" OE2 GLU A 20 " pdb=" NZ LYS C 80 " model vdw 1.681 3.120 nonbonded pdb=" CE LYS A 10 " pdb=" OE2 GLU C 35 " model vdw 1.695 3.440 nonbonded pdb=" OE2 GLU D 35 " pdb=" CE LYS E 10 " model vdw 1.730 3.440 nonbonded pdb=" OE2 GLU E 35 " pdb=" CE LYS F 10 " model vdw 1.730 3.440 nonbonded pdb=" OE2 GLU A 35 " pdb=" CE LYS B 10 " model vdw 1.730 3.440 ... (remaining 26000 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.270 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5326 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 : 0.016 0.390 3798 Z= 1.558 Angle : 0.680 4.970 5106 Z= 0.368 Chirality : 0.058 0.177 660 Planarity : 0.001 0.004 630 Dihedral : 9.633 50.740 1290 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 53.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -4.11 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.004 0.001 PHE B 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 ( 3786) covalent geometry : angle 0.67609 / 0.37 ( 5094) hydrogen bonds : bond 0.24446 / 16.79 ( 49) hydrogen bonds : angle 8.53897 / 5.25 ( 147) Misc. bond : bond 0.38959 / 27.53 ( 6) link_NAG-SER : bond 0.03628 / 2.55 ( 6) link_NAG-SER : angle 1.62480 / 0.81 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.024 Fit side-chains REVERT: A 22 THR cc_start: 0.8470 (m) cc_final: 0.8055 (p) REVERT: A 62 GLN cc_start: 0.8701 (mt0) cc_final: 0.8076 (tt0) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0673 time to fit residues: 1.6418 Evaluate side-chains 13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 9.9990 chunk 48 optimal weight: 0.0070 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 50 optimal weight: 0.0770 chunk 53 optimal weight: 0.0980 chunk 19 optimal weight: 0.0270 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.143036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.121206 restraints weight = 2381.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.123092 restraints weight = 1786.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124453 restraints weight = 1446.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.125434 restraints weight = 1225.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.126237 restraints weight = 1079.655| |-----------------------------------------------------------------------------| r_work (final): 0.3918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5204 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3798 Z= 0.152 Angle : 0.958 7.732 5106 Z= 0.514 Chirality : 0.067 0.323 660 Planarity : 0.002 0.010 630 Dihedral : 6.129 22.399 540 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.90 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR B 39 PHE 0.000 0.000 PHE F 94 HIS 0.000 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 3786) covalent geometry : angle 0.95787 / 0.51 ( 5094) hydrogen bonds : bond 0.14296 / 10.07 ( 49) hydrogen bonds : angle 6.82540 / 4.24 ( 147) Misc. bond : bond 0.00066 / 0.05 ( 6) link_NAG-SER : bond 0.00323 / 0.23 ( 6) link_NAG-SER : angle 0.82646 / 0.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.015 Fit side-chains REVERT: B 20 GLU cc_start: 0.7217 (tp30) cc_final: 0.6588 (pp20) REVERT: B 32 LYS cc_start: 0.4111 (mmmt) cc_final: 0.3908 (mmmt) REVERT: B 62 GLN cc_start: 0.8663 (mt0) cc_final: 0.8024 (tt0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0360 time to fit residues: 0.6628 Evaluate side-chains 14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 40 optimal weight: 0.0050 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 30.0000 chunk 44 optimal weight: 0.0030 chunk 35 optimal weight: 0.3980 chunk 41 optimal weight: 0.0000 chunk 22 optimal weight: 30.0000 chunk 12 optimal weight: 0.4980 overall best weight: 0.1008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.139897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.122913 restraints weight = 2238.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.124691 restraints weight = 1579.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.126028 restraints weight = 1235.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.126962 restraints weight = 1019.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.127777 restraints weight = 890.666| |-----------------------------------------------------------------------------| r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5302 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3798 Z= 0.126 Angle : 0.696 5.347 5106 Z= 0.386 Chirality : 0.060 0.285 660 Planarity : 0.002 0.006 630 Dihedral : 5.914 19.846 540 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 1.67 % Allowed : 3.33 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR E 39 PHE 0.000 0.000 PHE F 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 3786) covalent geometry : angle 0.69664 / 0.39 ( 5094) hydrogen bonds : bond 0.11869 / 8.41 ( 49) hydrogen bonds : angle 7.00507 / 4.48 ( 147) Misc. bond : bond 0.00019 / 0.01 ( 6) link_NAG-SER : bond 0.00300 / 0.21 ( 6) link_NAG-SER : angle 0.17154 / 0.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 20 time to evaluate : 0.014 Fit side-chains REVERT: B 20 GLU cc_start: 0.7396 (tp30) cc_final: 0.6781 (pp20) REVERT: B 62 GLN cc_start: 0.8648 (mt0) cc_final: 0.8109 (tt0) outliers start: 1 outliers final: 0 residues processed: 20 average time/residue: 0.0657 time to fit residues: 1.3906 Evaluate side-chains 13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.0060 chunk 35 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 10 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.140910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.120427 restraints weight = 2458.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.122095 restraints weight = 1887.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.123381 restraints weight = 1545.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.124409 restraints weight = 1319.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.125229 restraints weight = 1163.116| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5420 moved from start: 0.4882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3798 Z= 0.141 Angle : 0.902 8.265 5106 Z= 0.487 Chirality : 0.061 0.232 660 Planarity : 0.002 0.009 630 Dihedral : 6.297 24.153 540 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -3.82 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.005 TYR B 39 PHE 0.003 0.001 PHE A 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 3786) covalent geometry : angle 0.90119 / 0.49 ( 5094) hydrogen bonds : bond 0.10823 / 7.61 ( 49) hydrogen bonds : angle 6.63364 / 4.26 ( 147) Misc. bond : bond 0.00001 / 0.00 ( 6) link_NAG-SER : bond 0.00234 / 0.17 ( 6) link_NAG-SER : angle 1.19010 / 0.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.020 Fit side-chains REVERT: B 20 GLU cc_start: 0.7557 (tp30) cc_final: 0.6881 (pp20) REVERT: B 32 LYS cc_start: 0.3796 (mmmt) cc_final: 0.3594 (mmmt) REVERT: B 62 GLN cc_start: 0.8671 (mt0) cc_final: 0.8043 (tt0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0646 time to fit residues: 1.1846 Evaluate side-chains 14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 25 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.147795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.131580 restraints weight = 2075.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.133453 restraints weight = 1406.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.134947 restraints weight = 1073.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.136043 restraints weight = 868.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.136769 restraints weight = 737.480| |-----------------------------------------------------------------------------| r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5288 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3798 Z= 0.111 Angle : 0.764 7.165 5106 Z= 0.411 Chirality : 0.060 0.244 660 Planarity : 0.002 0.012 630 Dihedral : 6.086 24.093 540 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % 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: -3.71 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR D 39 PHE 0.000 0.000 PHE A 94 HIS 0.000 0.000 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 ( 3786) covalent geometry : angle 0.76508 / 0.41 ( 5094) hydrogen bonds : bond 0.09980 / 6.95 ( 49) hydrogen bonds : angle 6.88116 / 4.45 ( 147) Misc. bond : bond 0.00007 / 0.01 ( 6) link_NAG-SER : bond 0.00247 / 0.17 ( 6) link_NAG-SER : angle 0.17419 / 0.09 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.024 Fit side-chains REVERT: B 20 GLU cc_start: 0.7625 (tp30) cc_final: 0.7025 (pp20) REVERT: B 62 GLN cc_start: 0.8754 (mt0) cc_final: 0.8138 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0528 time to fit residues: 1.0839 Evaluate side-chains 14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 1 optimal weight: 0.1980 chunk 49 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.134000 restraints weight = 2462.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135979 restraints weight = 1816.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.137492 restraints weight = 1453.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.138557 restraints weight = 1221.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.139346 restraints weight = 1069.756| |-----------------------------------------------------------------------------| r_work (final): 0.3974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.5606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3798 Z= 0.137 Angle : 0.973 9.857 5106 Z= 0.510 Chirality : 0.062 0.265 660 Planarity : 0.003 0.018 630 Dihedral : 6.014 25.794 540 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -3.71 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR C 39 PHE 0.001 0.000 PHE C 94 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 3786) covalent geometry : angle 0.97165 / 0.51 ( 5094) hydrogen bonds : bond 0.09681 / 6.65 ( 49) hydrogen bonds : angle 6.81363 / 4.42 ( 147) Misc. bond : bond 0.00143 / 0.10 ( 6) link_NAG-SER : bond 0.00185 / 0.13 ( 6) link_NAG-SER : angle 1.30369 / 0.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.023 Fit side-chains REVERT: B 20 GLU cc_start: 0.7621 (tp30) cc_final: 0.6931 (pp20) REVERT: B 62 GLN cc_start: 0.8759 (mt0) cc_final: 0.8133 (tt0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0461 time to fit residues: 0.9071 Evaluate side-chains 14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 42 optimal weight: 10.0000 chunk 46 optimal weight: 0.0870 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 37 optimal weight: 0.3980 chunk 52 optimal weight: 7.9990 chunk 20 optimal weight: 0.0370 chunk 47 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.150259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.139492 restraints weight = 2940.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.140782 restraints weight = 2147.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.141684 restraints weight = 1724.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.142384 restraints weight = 1469.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.142919 restraints weight = 1297.063| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3798 Z= 0.189 Angle : 1.244 18.238 5106 Z= 0.641 Chirality : 0.063 0.249 660 Planarity : 0.003 0.012 630 Dihedral : 6.352 18.827 540 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.99 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR D 39 PHE 0.000 0.000 PHE C 94 HIS 0.000 0.000 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 ( 3786) covalent geometry : angle 1.24486 / 0.64 ( 5094) hydrogen bonds : bond 0.09592 / 6.47 ( 49) hydrogen bonds : angle 6.82841 / 4.43 ( 147) Misc. bond : bond 0.00308 / 0.22 ( 6) link_NAG-SER : bond 0.00125 / 0.09 ( 6) link_NAG-SER : angle 0.36657 / 0.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 20 time to evaluate : 0.025 Fit side-chains REVERT: C 72 THR cc_start: 0.7406 (p) cc_final: 0.7164 (p) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0511 time to fit residues: 1.0875 Evaluate side-chains 13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.0470 chunk 44 optimal weight: 0.2980 chunk 0 optimal weight: 9.9990 chunk 13 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.144577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.129776 restraints weight = 2321.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.131823 restraints weight = 1593.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.133058 restraints weight = 1212.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.133984 restraints weight = 998.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.134686 restraints weight = 863.486| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.6889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 3798 Z= 0.273 Angle : 1.304 16.866 5106 Z= 0.662 Chirality : 0.061 0.193 660 Planarity : 0.003 0.009 630 Dihedral : 7.165 33.427 540 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 1.67 % Allowed : 3.33 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.12 % 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: -3.88 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.006 TYR F 39 PHE 0.001 0.000 PHE F 94 HIS 0.000 0.000 HIS E 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.27 ( 3786) covalent geometry : angle 1.30298 / 0.66 ( 5094) hydrogen bonds : bond 0.10097 / 6.21 ( 49) hydrogen bonds : angle 7.77306 / 4.89 ( 147) Misc. bond : bond 0.00687 / 0.49 ( 6) link_NAG-SER : bond 0.00107 / 0.08 ( 6) link_NAG-SER : angle 1.59037 / 0.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.015 Fit side-chains REVERT: C 20 GLU cc_start: 0.8229 (pp20) cc_final: 0.7252 (tp30) REVERT: C 32 LYS cc_start: 0.3555 (mmmt) cc_final: 0.3196 (mmmt) REVERT: C 61 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7530 (mp0) REVERT: C 70 VAL cc_start: 0.8426 (m) cc_final: 0.8133 (t) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 0.0596 time to fit residues: 1.1489 Evaluate side-chains 13 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 35 optimal weight: 0.0000 chunk 30 optimal weight: 0.0000 chunk 33 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 47 optimal weight: 0.0870 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 overall best weight: 3.8170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.139006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.121110 restraints weight = 2266.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.122832 restraints weight = 1664.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.124185 restraints weight = 1338.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.125214 restraints weight = 1126.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.125964 restraints weight = 982.218| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.6579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 3798 Z= 0.214 Angle : 1.347 12.889 5106 Z= 0.696 Chirality : 0.068 0.299 660 Planarity : 0.004 0.032 630 Dihedral : 6.697 27.405 540 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % 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: -3.68 (0.31), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR F 39 PHE 0.003 0.001 PHE D 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 ( 3786) covalent geometry : angle 1.34780 / 0.70 ( 5094) hydrogen bonds : bond 0.10478 / 6.85 ( 49) hydrogen bonds : angle 6.89409 / 4.40 ( 147) Misc. bond : bond 0.00953 / 0.67 ( 6) link_NAG-SER : bond 0.00007 / 0.00 ( 6) link_NAG-SER : angle 1.05228 / 0.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.017 Fit side-chains REVERT: B 20 GLU cc_start: 0.8901 (pp20) cc_final: 0.7632 (tp30) REVERT: B 24 GLN cc_start: 0.6988 (pp30) cc_final: 0.6667 (pp30) REVERT: B 58 LYS cc_start: 0.7953 (tmmt) cc_final: 0.6621 (mmmt) REVERT: B 70 VAL cc_start: 0.8467 (m) cc_final: 0.8230 (t) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0383 time to fit residues: 0.7891 Evaluate side-chains 15 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 9 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 50 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.139110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.127705 restraints weight = 2708.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.129252 restraints weight = 1892.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.130444 restraints weight = 1469.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.131146 restraints weight = 1211.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.131842 restraints weight = 1064.450| |-----------------------------------------------------------------------------| r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5941 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 3798 Z= 0.241 Angle : 1.298 11.358 5106 Z= 0.678 Chirality : 0.065 0.209 660 Planarity : 0.004 0.021 630 Dihedral : 7.449 34.623 540 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.12 % 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: -3.95 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR C 39 PHE 0.003 0.001 PHE F 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00621 / 0.24 ( 3786) covalent geometry : angle 1.29856 / 0.68 ( 5094) hydrogen bonds : bond 0.10882 / 7.54 ( 49) hydrogen bonds : angle 6.41915 / 4.15 ( 147) Misc. bond : bond 0.00802 / 0.57 ( 6) link_NAG-SER : bond 0.00199 / 0.14 ( 6) link_NAG-SER : angle 0.76069 / 0.39 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.022 Fit side-chains REVERT: C 20 GLU cc_start: 0.8542 (pp20) cc_final: 0.7646 (tp30) REVERT: C 23 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7487 (tmtt) REVERT: C 24 GLN cc_start: 0.7491 (pp30) cc_final: 0.6512 (pp30) REVERT: C 58 LYS cc_start: 0.7882 (tmmt) cc_final: 0.6640 (mmmt) REVERT: C 61 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7775 (tm-30) REVERT: C 70 VAL cc_start: 0.8595 (m) cc_final: 0.8368 (t) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0491 time to fit residues: 1.0138 Evaluate side-chains 17 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 0 optimal weight: 9.9990 chunk 29 optimal weight: 0.0970 chunk 16 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 11 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 20.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.123818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.111742 restraints weight = 2540.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.113415 restraints weight = 1772.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.114650 restraints weight = 1358.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.115434 restraints weight = 1106.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.116230 restraints weight = 954.243| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.6658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 3798 Z= 0.254 Angle : 1.214 9.239 5106 Z= 0.639 Chirality : 0.064 0.193 660 Planarity : 0.004 0.015 630 Dihedral : 7.622 31.498 540 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 22.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.12 % 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: -4.03 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.003 TYR D 39 PHE 0.005 0.001 PHE D 94 HIS 0.009 0.006 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00641 / 0.25 ( 3786) covalent geometry : angle 1.21396 / 0.64 ( 5094) hydrogen bonds : bond 0.11405 / 7.77 ( 49) hydrogen bonds : angle 6.32626 / 4.03 ( 147) Misc. bond : bond 0.00685 / 0.48 ( 6) link_NAG-SER : bond 0.00118 / 0.08 ( 6) link_NAG-SER : angle 1.17623 / 0.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 630.81 seconds wall clock time: 11 minutes 34.47 seconds (694.47 seconds total)