Starting phenix.real_space_refine on Wed Mar 5 22:09:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gf7_29980/03_2025/8gf7_29980.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gf7_29980/03_2025/8gf7_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_29980/03_2025/8gf7_29980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gf7_29980/03_2025/8gf7_29980.map" model { file = "/net/cci-nas-00/data/ceres_data/8gf7_29980/03_2025/8gf7_29980.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gf7_29980/03_2025/8gf7_29980.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.18, per 1000 atoms: 0.58 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: 0.94 Conformation dependent library (CDL) restraints added in 477.4 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: 0.59 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: 1.25 Time building geometry restraints manager: 1.10 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: 2070 10.15 - 20.30: 168 20.30 - 30.44: 60 30.44 - 40.59: 12 40.59 - 50.74: 18 Dihedral angle restraints: 2328 sinusoidal: 876 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 2325 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.850 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5169 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 : 0.003 0.027 3786 Z= 0.197 Angle : 0.676 4.970 5094 Z= 0.368 Chirality : 0.058 0.177 660 Planarity : 0.001 0.004 630 Dihedral : 10.147 50.740 1416 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.002 0.001 HIS D 50 PHE 0.004 0.001 PHE B 94 TYR 0.002 0.001 TYR B 39 *********************** 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 : 0.065 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: 0.1640 time to fit residues: 4.0012 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 10.0000 chunk 40 optimal weight: 0.0270 chunk 22 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 overall best weight: 3.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3978 r_free = 0.3978 target = 0.132876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.113731 restraints weight = 2411.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115380 restraints weight = 1761.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.116768 restraints weight = 1419.647| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5490 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3786 Z= 0.260 Angle : 0.954 6.941 5094 Z= 0.516 Chirality : 0.067 0.313 660 Planarity : 0.003 0.011 630 Dihedral : 9.469 56.039 666 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.004 0.001 PHE D 94 TYR 0.002 0.001 TYR C 39 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.064 Fit side-chains REVERT: B 20 GLU cc_start: 0.7422 (tp30) cc_final: 0.6967 (pp20) REVERT: B 32 LYS cc_start: 0.4445 (mmmt) cc_final: 0.3992 (mmmt) REVERT: B 62 GLN cc_start: 0.8619 (mt0) cc_final: 0.8047 (tt0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1712 time to fit residues: 2.9303 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 : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 35 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 40 optimal weight: 0.1980 chunk 2 optimal weight: 0.2980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.129267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.113344 restraints weight = 2388.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.115291 restraints weight = 1596.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.116776 restraints weight = 1198.134| |-----------------------------------------------------------------------------| r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3786 Z= 0.178 Angle : 0.729 5.010 5094 Z= 0.405 Chirality : 0.061 0.278 660 Planarity : 0.002 0.006 630 Dihedral : 9.844 59.958 666 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 1.67 % Allowed : 6.67 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.26), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE E 94 TYR 0.003 0.001 TYR B 39 *********************** 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. ------------------------------------------------------------------------------- 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: 1 poor density : 16 time to evaluate : 0.071 Fit side-chains REVERT: B 20 GLU cc_start: 0.7622 (tp30) cc_final: 0.7009 (pp20) REVERT: B 21 LYS cc_start: 0.8949 (pttt) cc_final: 0.8670 (ptmt) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.1429 time to fit residues: 2.4742 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 : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 53 optimal weight: 0.0980 chunk 47 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 1 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 4.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.132698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.113964 restraints weight = 2585.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115876 restraints weight = 1797.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.117149 restraints weight = 1381.115| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5368 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3786 Z= 0.280 Angle : 0.901 8.015 5094 Z= 0.492 Chirality : 0.060 0.242 660 Planarity : 0.002 0.009 630 Dihedral : 9.656 55.542 666 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 16.54 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 50 PHE 0.004 0.001 PHE E 94 TYR 0.003 0.001 TYR A 39 *********************** 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. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.067 Fit side-chains REVERT: B 20 GLU cc_start: 0.7943 (tp30) cc_final: 0.7142 (pm20) REVERT: B 32 LYS cc_start: 0.4258 (mmmt) cc_final: 0.4048 (mmmt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1522 time to fit residues: 2.6381 Evaluate side-chains 12 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 37 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.114998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.103418 restraints weight = 2684.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.105068 restraints weight = 1702.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.106383 restraints weight = 1257.410| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3786 Z= 0.301 Angle : 0.957 6.487 5094 Z= 0.532 Chirality : 0.064 0.249 660 Planarity : 0.003 0.014 630 Dihedral : 10.408 59.694 666 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % Rotamer: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.007 0.002 PHE B 94 TYR 0.004 0.001 TYR E 39 *********************** 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. ------------------------------------------------------------------------------- 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 : 0.062 Fit side-chains REVERT: B 20 GLU cc_start: 0.7942 (tp30) cc_final: 0.7337 (pm20) REVERT: B 21 LYS cc_start: 0.8867 (ptmt) cc_final: 0.8665 (pttt) REVERT: B 23 LYS cc_start: 0.8039 (tmtt) cc_final: 0.7674 (tmtt) REVERT: B 24 GLN cc_start: 0.7314 (pp30) cc_final: 0.6708 (pp30) REVERT: B 72 THR cc_start: 0.7906 (p) cc_final: 0.7599 (p) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1557 time to fit residues: 2.8439 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 : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 8.9990 chunk 26 optimal weight: 0.0060 chunk 51 optimal weight: 30.0000 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 16 optimal weight: 8.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.132794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.118786 restraints weight = 2105.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.121309 restraints weight = 1213.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.122990 restraints weight = 825.234| |-----------------------------------------------------------------------------| r_work (final): 0.3941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5779 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3786 Z= 0.272 Angle : 1.141 10.618 5094 Z= 0.587 Chirality : 0.065 0.289 660 Planarity : 0.002 0.010 630 Dihedral : 9.702 56.743 666 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.26), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.000 0.000 PHE D 94 TYR 0.005 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 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 : 0.055 Fit side-chains REVERT: C 20 GLU cc_start: 0.7675 (tp30) cc_final: 0.7386 (pm20) REVERT: C 23 LYS cc_start: 0.7699 (tmtt) cc_final: 0.7414 (tmtt) REVERT: C 24 GLN cc_start: 0.7669 (pp30) cc_final: 0.6998 (pp30) REVERT: C 32 LYS cc_start: 0.4451 (mmmt) cc_final: 0.4204 (mmmt) REVERT: C 57 GLU cc_start: 0.8830 (tp30) cc_final: 0.8047 (tm-30) REVERT: C 70 VAL cc_start: 0.8591 (m) cc_final: 0.8351 (t) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1512 time to fit residues: 3.0708 Evaluate side-chains 16 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 0.0060 chunk 22 optimal weight: 0.0370 chunk 21 optimal weight: 0.0040 chunk 2 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 47 optimal weight: 0.6980 chunk 41 optimal weight: 8.9990 chunk 3 optimal weight: 0.0040 chunk 34 optimal weight: 0.0010 chunk 50 optimal weight: 0.0980 overall best weight: 0.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.132511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118359 restraints weight = 2416.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.120335 restraints weight = 1678.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.121687 restraints weight = 1265.474| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5212 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3786 Z= 0.203 Angle : 0.785 5.769 5094 Z= 0.420 Chirality : 0.060 0.286 660 Planarity : 0.002 0.013 630 Dihedral : 9.474 57.538 666 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.26), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.001 0.000 PHE C 94 TYR 0.006 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 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 : 0.065 Fit side-chains REVERT: B 20 GLU cc_start: 0.7833 (tp30) cc_final: 0.7282 (pm20) REVERT: B 21 LYS cc_start: 0.8470 (ptmt) cc_final: 0.8207 (tptp) REVERT: B 57 GLU cc_start: 0.8894 (tp30) cc_final: 0.8647 (tp30) REVERT: B 70 VAL cc_start: 0.8524 (m) cc_final: 0.8266 (t) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1318 time to fit residues: 2.7108 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 : 0.070 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 8.9990 chunk 12 optimal weight: 0.3980 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.4980 chunk 24 optimal weight: 40.0000 chunk 20 optimal weight: 0.4980 chunk 46 optimal weight: 0.0010 chunk 45 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.133132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118022 restraints weight = 2176.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.119617 restraints weight = 1558.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.120784 restraints weight = 1230.134| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5547 moved from start: 0.6111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3786 Z= 0.229 Angle : 0.895 9.616 5094 Z= 0.467 Chirality : 0.060 0.273 660 Planarity : 0.002 0.012 630 Dihedral : 9.331 54.782 666 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % 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 : 1.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS E 50 PHE 0.001 0.000 PHE D 94 TYR 0.004 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 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 : 0.069 Fit side-chains REVERT: B 20 GLU cc_start: 0.7735 (tp30) cc_final: 0.7406 (pm20) REVERT: B 24 GLN cc_start: 0.7627 (pp30) cc_final: 0.7363 (pp30) REVERT: B 32 LYS cc_start: 0.4668 (mmmt) cc_final: 0.4311 (mmmt) REVERT: B 57 GLU cc_start: 0.8878 (tp30) cc_final: 0.8635 (tp30) REVERT: B 70 VAL cc_start: 0.8479 (m) cc_final: 0.8231 (t) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1503 time to fit residues: 2.7721 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 : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 9.9990 chunk 41 optimal weight: 0.4980 chunk 15 optimal weight: 30.0000 chunk 53 optimal weight: 0.0980 chunk 27 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 30 optimal weight: 0.4980 chunk 42 optimal weight: 20.0000 chunk 11 optimal weight: 0.0010 chunk 8 optimal weight: 0.2980 chunk 9 optimal weight: 10.0000 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.142669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.130552 restraints weight = 2572.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.132186 restraints weight = 1810.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.133289 restraints weight = 1423.863| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5599 moved from start: 0.6500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3786 Z= 0.228 Angle : 0.888 7.226 5094 Z= 0.467 Chirality : 0.059 0.274 660 Planarity : 0.003 0.016 630 Dihedral : 9.683 54.516 666 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 50 PHE 0.000 0.000 PHE E 94 TYR 0.023 0.008 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** 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 : 0.068 Fit side-chains REVERT: C 20 GLU cc_start: 0.7756 (tp30) cc_final: 0.7216 (pm20) REVERT: C 24 GLN cc_start: 0.7824 (pp30) cc_final: 0.7117 (pp30) REVERT: C 57 GLU cc_start: 0.8895 (tp30) cc_final: 0.8645 (tp30) REVERT: C 70 VAL cc_start: 0.8436 (m) cc_final: 0.8193 (t) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.1581 time to fit residues: 2.3894 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 : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 9 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 0.2980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4044 r_free = 0.4044 target = 0.132176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.122497 restraints weight = 2896.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.123745 restraints weight = 2109.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.124676 restraints weight = 1669.585| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5790 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3786 Z= 0.298 Angle : 0.949 10.927 5094 Z= 0.501 Chirality : 0.060 0.246 660 Planarity : 0.002 0.016 630 Dihedral : 9.447 52.429 666 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 50 PHE 0.003 0.001 PHE A 94 TYR 0.009 0.002 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 704 Ramachandran restraints generated. 352 Oldfield, 0 Emsley, 352 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 : 0.071 Fit side-chains REVERT: B 20 GLU cc_start: 0.7914 (tp30) cc_final: 0.7523 (pm20) REVERT: B 70 VAL cc_start: 0.8645 (m) cc_final: 0.8387 (t) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1475 time to fit residues: 2.6980 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 : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 15 optimal weight: 0.0030 chunk 29 optimal weight: 10.0000 chunk 37 optimal weight: 0.0050 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 38 optimal weight: 0.0040 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 6 optimal weight: 0.0030 chunk 35 optimal weight: 0.5980 overall best weight: 0.1026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.137853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.126253 restraints weight = 2717.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.127449 restraints weight = 2081.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.128353 restraints weight = 1718.703| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5271 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 3786 Z= 0.356 Angle : 0.979 11.434 5094 Z= 0.514 Chirality : 0.058 0.204 660 Planarity : 0.003 0.016 630 Dihedral : 9.726 54.750 666 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % 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 : 1.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.000 0.000 PHE E 94 TYR 0.007 0.003 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1236.96 seconds wall clock time: 22 minutes 25.98 seconds (1345.98 seconds total)