Starting phenix.real_space_refine on Thu Nov 14 04:01:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/11_2024/8gf7_29980.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/11_2024/8gf7_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/11_2024/8gf7_29980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/11_2024/8gf7_29980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/11_2024/8gf7_29980.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/11_2024/8gf7_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-5513/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: 2.30, per 1000 atoms: 0.61 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=0, 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 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 462.1 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: 0.68 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: 0.95 Time building geometry restraints manager: 1.01 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: 53 2.32 - 2.97: 1747 2.97 - 3.61: 5082 3.61 - 4.26: 7164 4.26 - 4.90: 11983 Nonbonded interactions: 26029 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 26024 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: 0.00 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: 1.560 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: 0.020 Set scattering table: 0.040 Process input model: 13.020 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- 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= 0.196 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 : 0.062 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: 0.1833 time to fit residues: 4.4400 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=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 ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5530 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3786 Z= 0.259 Angle : 0.946 6.981 5094 Z= 0.515 Chirality : 0.069 0.348 660 Planarity : 0.003 0.012 630 Dihedral : 9.376 54.789 666 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % 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 (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: -3.96 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 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: 1 poor density : 15 time to evaluate : 0.072 Fit side-chains REVERT: B 20 GLU cc_start: 0.7112 (tp30) cc_final: 0.6828 (pp20) REVERT: B 32 LYS cc_start: 0.4192 (mmmt) cc_final: 0.3733 (mmmt) REVERT: B 62 GLN cc_start: 0.8659 (mt0) cc_final: 0.8085 (tt0) outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1401 time to fit residues: 2.4372 Evaluate side-chains 14 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 13 optimal weight: 30.0000 chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 48 optimal weight: 0.1980 chunk 16 optimal weight: 10.0000 chunk 39 optimal weight: 0.0040 overall best weight: 4.0434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5615 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3786 Z= 0.220 Angle : 0.728 5.326 5094 Z= 0.412 Chirality : 0.065 0.339 660 Planarity : 0.002 0.007 630 Dihedral : 9.800 58.056 666 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 1.67 % Allowed : 5.00 % 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: -4.11 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.13 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.004 0.001 PHE C 94 TYR 0.003 0.001 TYR E 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: 0.7638 (tp30) cc_final: 0.6953 (pm20) REVERT: B 21 LYS cc_start: 0.8934 (pttt) cc_final: 0.8663 (ptmt) outliers start: 1 outliers final: 0 residues processed: 16 average time/residue: 0.1400 time to fit residues: 2.4308 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 : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 0.0470 chunk 36 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 5 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 14 optimal weight: 0.0070 chunk 43 optimal weight: 9.9990 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.4855 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= 0.246 Angle : 0.854 8.551 5094 Z= 0.466 Chirality : 0.062 0.262 660 Planarity : 0.003 0.013 630 Dihedral : 9.763 58.042 666 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % 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: -4.04 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.000 0.000 PHE F 94 TYR 0.005 0.002 TYR F 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 19 residues out of total 60 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.070 Fit side-chains REVERT: B 20 GLU cc_start: 0.7828 (tp30) cc_final: 0.7199 (pm20) REVERT: B 32 LYS cc_start: 0.4689 (mmmt) cc_final: 0.4378 (mmmt) REVERT: B 62 GLN cc_start: 0.8730 (mt0) cc_final: 0.8148 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1380 time to fit residues: 2.8331 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 : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 44 optimal weight: 0.0010 chunk 36 optimal weight: 10.0000 chunk 26 optimal weight: 0.0470 chunk 46 optimal weight: 9.9990 chunk 13 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5582 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3786 Z= 0.214 Angle : 0.897 6.896 5094 Z= 0.486 Chirality : 0.064 0.319 660 Planarity : 0.002 0.010 630 Dihedral : 9.738 59.603 666 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % 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: -3.73 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.002 0.001 PHE A 94 TYR 0.020 0.006 TYR D 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 : 0.073 Fit side-chains REVERT: B 20 GLU cc_start: 0.7832 (tp30) cc_final: 0.7275 (pm20) REVERT: B 32 LYS cc_start: 0.4714 (mmmt) cc_final: 0.4436 (mmmt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1522 time to fit residues: 2.7951 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 : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 20.0000 chunk 30 optimal weight: 0.3980 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 30.0000 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5543 moved from start: 0.5435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3786 Z= 0.258 Angle : 1.013 9.027 5094 Z= 0.534 Chirality : 0.065 0.332 660 Planarity : 0.002 0.010 630 Dihedral : 9.183 55.210 666 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 18.45 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: -4.00 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.002 0.001 PHE D 94 TYR 0.002 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.085 Fit side-chains REVERT: B 20 GLU cc_start: 0.7838 (tp30) cc_final: 0.7320 (pm20) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1447 time to fit residues: 2.6826 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 : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0470 chunk 38 optimal weight: 0.0070 chunk 43 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.0030 chunk 31 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 10 optimal weight: 0.2980 chunk 33 optimal weight: 0.0470 overall best weight: 0.0404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3786 Z= 0.225 Angle : 0.852 8.579 5094 Z= 0.459 Chirality : 0.063 0.274 660 Planarity : 0.002 0.010 630 Dihedral : 9.913 59.043 666 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % 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 (0.28), 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 0.001 0.000 HIS D 50 PHE 0.000 0.000 PHE A 94 TYR 0.000 0.000 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.073 Fit side-chains REVERT: B 20 GLU cc_start: 0.7805 (tp30) cc_final: 0.7497 (pp20) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1217 time to fit residues: 2.5319 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 : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 47 optimal weight: 0.0570 chunk 49 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 3.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.6012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 3786 Z= 0.319 Angle : 0.927 7.422 5094 Z= 0.502 Chirality : 0.064 0.306 660 Planarity : 0.002 0.014 630 Dihedral : 9.418 53.603 666 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.35 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: -4.05 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.08 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.003 0.001 PHE A 94 TYR 0.004 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.063 Fit side-chains REVERT: B 20 GLU cc_start: 0.7828 (tp30) cc_final: 0.7432 (pm20) REVERT: B 24 GLN cc_start: 0.7413 (pp30) cc_final: 0.7181 (pp30) REVERT: B 62 GLN cc_start: 0.8618 (mt0) cc_final: 0.8076 (tt0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1121 time to fit residues: 2.2187 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 : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 8.9990 chunk 51 optimal weight: 0.0010 chunk 24 optimal weight: 9.9990 chunk 35 optimal weight: 0.0980 chunk 53 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3786 Z= 0.233 Angle : 0.981 10.030 5094 Z= 0.519 Chirality : 0.066 0.352 660 Planarity : 0.002 0.014 630 Dihedral : 9.770 58.442 666 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 19.35 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: -3.85 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.002 0.001 PHE D 94 TYR 0.002 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.073 Fit side-chains REVERT: B 20 GLU cc_start: 0.7796 (tp30) cc_final: 0.7447 (pm20) REVERT: B 23 LYS cc_start: 0.7809 (tmtt) cc_final: 0.7551 (tmtt) REVERT: B 24 GLN cc_start: 0.7544 (pp30) cc_final: 0.6804 (pp30) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1570 time to fit residues: 3.2181 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 : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 26 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 0.0570 chunk 42 optimal weight: 20.0000 chunk 17 optimal weight: 0.9990 overall best weight: 1.4704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5486 moved from start: 0.6190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 3786 Z= 0.339 Angle : 1.215 12.722 5094 Z= 0.604 Chirality : 0.063 0.306 660 Planarity : 0.002 0.015 630 Dihedral : 9.601 54.819 666 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % 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: -3.97 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 50 PHE 0.001 0.000 PHE A 94 TYR 0.001 0.001 TYR D 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- 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 : 0.065 Fit side-chains REVERT: B 20 GLU cc_start: 0.7755 (tp30) cc_final: 0.7331 (pm20) REVERT: B 21 LYS cc_start: 0.8911 (pttt) cc_final: 0.7964 (mmtt) REVERT: B 24 GLN cc_start: 0.7703 (pp30) cc_final: 0.6973 (pp30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1261 time to fit residues: 2.3310 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 : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 37 optimal weight: 0.0060 chunk 2 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 28 optimal weight: 0.0870 chunk 36 optimal weight: 9.9990 chunk 1 optimal weight: 0.4980 chunk 34 optimal weight: 10.0000 overall best weight: 0.4974 ------------------------------------------------------------------------------- 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 = 0.4032 r_free = 0.4032 target = 0.131901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.116402 restraints weight = 2068.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.118331 restraints weight = 1395.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.119631 restraints weight = 1052.369| |-----------------------------------------------------------------------------| r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5278 moved from start: 0.6374 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= 0.274 Angle : 0.996 11.022 5094 Z= 0.516 Chirality : 0.062 0.299 660 Planarity : 0.002 0.009 630 Dihedral : 9.354 55.659 666 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.77 % Favored : 85.23 % 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 (0.28), 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 0.000 0.000 HIS D 50 PHE 0.000 0.000 PHE E 94 TYR 0.001 0.000 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1197.33 seconds wall clock time: 22 minutes 28.79 seconds (1348.79 seconds total)