Starting phenix.real_space_refine on Sun Mar 10 18:04:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/03_2024/8gf7_29980.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/03_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_29980/03_2024/8gf7_29980.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/03_2024/8gf7_29980.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/03_2024/8gf7_29980.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gf7_29980/03_2024/8gf7_29980.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3774 Number of models: 1 Model: "" Number of chains: 12 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: "B" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 615 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "C" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 615 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "D" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 615 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "E" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 615 Classifications: {'peptide': 90} Link IDs: {'TRANS': 89} Chain: "F" 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Chain: "E" 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 Chain: "F" 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 Time building chain proxies: 2.38, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 1.43 Conformation dependent library (CDL) restraints added in 915.1 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: 0.59 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: 0.91 Time building geometry restraints manager: 1.54 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: 105.19 - 110.39: 987 110.39 - 115.60: 1701 115.60 - 120.81: 1110 120.81 - 126.02: 1290 126.02 - 131.22: 6 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 2.520 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 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: 1.360 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: 6.620 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.780 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.073 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: 0.1709 time to fit residues: 4.1672 Evaluate side-chains 13 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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: 6.9990 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- 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: 0.5605 moved from start: 0.4054 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= 0.265 Angle : 0.975 6.803 5094 Z= 0.533 Chirality : 0.068 0.328 660 Planarity : 0.003 0.011 630 Dihedral : 9.677 56.310 666 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 22.32 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: -4.06 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS B 50 PHE 0.005 0.002 PHE F 94 TYR 0.002 0.001 TYR B 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 15 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.054 Fit side-chains REVERT: B 20 GLU cc_start: 0.7485 (tp30) cc_final: 0.7195 (pp20) REVERT: B 32 LYS cc_start: 0.4452 (mmmt) cc_final: 0.3980 (mmmt) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.1218 time to fit residues: 1.9900 Evaluate side-chains 13 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.059 ------------------------------------------------------------------------------- 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: 0.0040 chunk 33 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 49 optimal weight: 0.0020 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.3404 ------------------------------------------------------------------------------- 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: 0.5558 moved from start: 0.4277 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= 0.187 Angle : 0.708 5.043 5094 Z= 0.400 Chirality : 0.065 0.351 660 Planarity : 0.002 0.008 630 Dihedral : 9.686 59.130 666 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 20.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 3.33 % Allowed : 3.33 % 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: -4.09 (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 0.001 0.001 HIS B 50 PHE 0.002 0.001 PHE A 94 TYR 0.003 0.001 TYR C 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 19 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.073 Fit side-chains REVERT: B 20 GLU cc_start: 0.7648 (tp30) cc_final: 0.7165 (pp20) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 0.1339 time to fit residues: 2.6207 Evaluate side-chains 14 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.073 ------------------------------------------------------------------------------- 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: 0.9980 chunk 36 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 5 optimal weight: 0.0050 chunk 23 optimal weight: 0.0040 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 46 optimal weight: 20.0000 chunk 14 optimal weight: 0.0050 chunk 43 optimal weight: 9.9990 overall best weight: 0.4022 ------------------------------------------------------------------------------- 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: 0.5503 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3786 Z= 0.213 Angle : 0.842 8.800 5094 Z= 0.460 Chirality : 0.062 0.275 660 Planarity : 0.003 0.015 630 Dihedral : 9.508 57.191 666 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.05 % Favored : 82.95 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % 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: -4.01 (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 0.000 0.000 HIS A 50 PHE 0.001 0.000 PHE D 94 TYR 0.004 0.002 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 15 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.071 Fit side-chains REVERT: B 20 GLU cc_start: 0.7799 (tp30) cc_final: 0.7406 (pp20) REVERT: B 58 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7503 (mmmt) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1475 time to fit residues: 2.4022 Evaluate side-chains 13 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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: 7.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 36 optimal weight: 9.9990 chunk 26 optimal weight: 0.0470 chunk 46 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 overall best weight: 0.9478 ------------------------------------------------------------------------------- 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: 0.5477 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 0.040 3786 Z= 0.229 Angle : 0.839 8.355 5094 Z= 0.449 Chirality : 0.061 0.287 660 Planarity : 0.002 0.009 630 Dihedral : 9.711 59.177 666 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % 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: -3.64 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.001 0.000 PHE D 94 TYR 0.004 0.002 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 18 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.076 Fit side-chains REVERT: B 20 GLU cc_start: 0.7781 (tp30) cc_final: 0.7462 (pp20) REVERT: B 35 GLU cc_start: 0.4011 (mt-10) cc_final: 0.3500 (mm-30) REVERT: B 58 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7281 (pptt) REVERT: B 62 GLN cc_start: 0.8717 (mt0) cc_final: 0.8171 (tt0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1078 time to fit residues: 2.1452 Evaluate side-chains 15 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 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 10 optimal weight: 0.0670 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 2.3924 ------------------------------------------------------------------------------- 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: 0.5520 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3786 Z= 0.198 Angle : 0.834 9.130 5094 Z= 0.458 Chirality : 0.063 0.296 660 Planarity : 0.002 0.009 630 Dihedral : 9.311 54.882 666 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 16.25 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 : 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: -3.83 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.002 0.001 PHE F 94 TYR 0.021 0.007 TYR A 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 19 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.064 Fit side-chains REVERT: B 20 GLU cc_start: 0.7865 (tp30) cc_final: 0.7516 (pp20) REVERT: B 58 LYS cc_start: 0.8284 (tmtt) cc_final: 0.7662 (pptt) REVERT: B 62 GLN cc_start: 0.8722 (mt0) cc_final: 0.8173 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1262 time to fit residues: 2.5893 Evaluate side-chains 17 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.063 ------------------------------------------------------------------------------- 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: 8.9990 chunk 38 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.5437 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3786 Z= 0.269 Angle : 0.950 8.550 5094 Z= 0.496 Chirality : 0.062 0.281 660 Planarity : 0.002 0.012 630 Dihedral : 9.807 58.580 666 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.64 % Favored : 86.36 % Rotamer: Outliers : 0.00 % Allowed : 8.33 % 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: -3.70 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 50 PHE 0.002 0.001 PHE E 94 TYR 0.003 0.001 TYR A 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 18 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.073 Fit side-chains REVERT: B 20 GLU cc_start: 0.7789 (tp30) cc_final: 0.7300 (pm20) REVERT: B 21 LYS cc_start: 0.8879 (pttt) cc_final: 0.8648 (ptmt) REVERT: B 58 LYS cc_start: 0.8232 (tmtt) cc_final: 0.7608 (pptt) REVERT: B 62 GLN cc_start: 0.8714 (mt0) cc_final: 0.8180 (tt0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1301 time to fit residues: 2.5443 Evaluate side-chains 14 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.074 ------------------------------------------------------------------------------- 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: 0.0770 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 40 optimal weight: 8.9990 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 0.0980 chunk 45 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 overall best weight: 5.4344 ------------------------------------------------------------------------------- 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: 0.5657 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3786 Z= 0.306 Angle : 0.942 9.436 5094 Z= 0.508 Chirality : 0.060 0.225 660 Planarity : 0.003 0.019 630 Dihedral : 9.255 53.528 666 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.91 % Favored : 84.09 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 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: -3.82 (0.30), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.23), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS C 50 PHE 0.005 0.001 PHE A 94 TYR 0.004 0.002 TYR C 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 fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.071 Fit side-chains REVERT: B 20 GLU cc_start: 0.7862 (tp30) cc_final: 0.7385 (pm20) REVERT: B 23 LYS cc_start: 0.7881 (tmtt) cc_final: 0.7530 (tmtt) REVERT: B 24 GLN cc_start: 0.7423 (pp30) cc_final: 0.6696 (pp30) REVERT: B 62 GLN cc_start: 0.8730 (mt0) cc_final: 0.8161 (tt0) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1581 time to fit residues: 3.0784 Evaluate side-chains 17 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.071 ------------------------------------------------------------------------------- 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: 6.9990 chunk 43 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 35 optimal weight: 0.0030 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 overall best weight: 2.0194 ------------------------------------------------------------------------------- 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: 0.5603 moved from start: 0.6349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 3786 Z= 0.294 Angle : 1.075 9.708 5094 Z= 0.564 Chirality : 0.063 0.189 660 Planarity : 0.003 0.018 630 Dihedral : 9.698 58.107 666 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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 : 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: -3.96 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS D 50 PHE 0.002 0.000 PHE F 94 TYR 0.002 0.001 TYR E 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 fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.072 Fit side-chains REVERT: B 12 LYS cc_start: 0.7277 (mmtt) cc_final: 0.5785 (pptt) REVERT: B 20 GLU cc_start: 0.7799 (tp30) cc_final: 0.7480 (pm20) REVERT: B 21 LYS cc_start: 0.8545 (ptmt) cc_final: 0.8295 (pttt) REVERT: B 24 GLN cc_start: 0.7529 (pp30) cc_final: 0.6808 (pp30) REVERT: B 62 GLN cc_start: 0.8712 (mt0) cc_final: 0.8157 (tt0) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1490 time to fit residues: 3.0447 Evaluate side-chains 16 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 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: 9.9990 chunk 33 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 chunk 42 optimal weight: 30.0000 chunk 17 optimal weight: 0.0000 overall best weight: 4.2004 ------------------------------------------------------------------------------- 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: 0.5756 moved from start: 0.6611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 3786 Z= 0.343 Angle : 1.039 8.512 5094 Z= 0.547 Chirality : 0.060 0.221 660 Planarity : 0.003 0.016 630 Dihedral : 9.197 53.074 666 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 22.06 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 : 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: -3.89 (0.29), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.004 0.001 PHE E 94 TYR 0.008 0.003 TYR F 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 19 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.071 Fit side-chains REVERT: B 12 LYS cc_start: 0.7302 (mmtt) cc_final: 0.5676 (pttm) REVERT: B 20 GLU cc_start: 0.7862 (tp30) cc_final: 0.7489 (pm20) REVERT: B 21 LYS cc_start: 0.8676 (ptmt) cc_final: 0.8258 (pttt) outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.1305 time to fit residues: 2.6959 Evaluate side-chains 18 residues out of total 60 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.070 ------------------------------------------------------------------------------- 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: 0.0670 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 37 optimal weight: 0.0060 chunk 2 optimal weight: 0.0070 chunk 30 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.0670 chunk 36 optimal weight: 10.0000 chunk 1 optimal weight: 0.0270 chunk 34 optimal weight: 9.9990 overall best weight: 0.0348 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.133153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.122073 restraints weight = 2827.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.123762 restraints weight = 1933.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.124958 restraints weight = 1439.411| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5713 moved from start: 0.6767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3786 Z= 0.247 Angle : 0.963 9.826 5094 Z= 0.510 Chirality : 0.059 0.195 660 Planarity : 0.003 0.017 630 Dihedral : 9.656 59.220 666 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -3.89 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (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 F 94 TYR 0.013 0.003 TYR C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.17 seconds wall clock time: 23 minutes 0.64 seconds (1380.64 seconds total)