Starting phenix.real_space_refine on Wed Sep 17 03:52:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckk_45650/09_2025/9ckk_45650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckk_45650/09_2025/9ckk_45650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ckk_45650/09_2025/9ckk_45650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckk_45650/09_2025/9ckk_45650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ckk_45650/09_2025/9ckk_45650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckk_45650/09_2025/9ckk_45650.map" } resolution = 2.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 2192 2.51 5 N 608 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3528 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "B" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "C" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "D" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "E" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "F" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "G" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "H" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 441 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Time building chain proxies: 1.19, per 1000 atoms: 0.34 Number of scatterers: 3528 At special positions: 0 Unit cell: (112.56, 80.64, 39.48, 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 728 8.00 N 608 7.00 C 2192 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.30 Conformation dependent library (CDL) restraints added in 161.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 76.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 21 removed outlier: 6.448A pdb=" N ALA A 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU C 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA A 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 49 removed outlier: 9.154A pdb=" N VAL A 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N VAL C 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N THR C 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N GLU C 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 52 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL C 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N THR A 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 37 through 49 removed outlier: 9.154A pdb=" N VAL A 37 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 10.053A pdb=" N VAL C 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 9.337A pdb=" N TYR A 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N SER C 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 8.967A pdb=" N GLY A 41 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 10.150A pdb=" N THR C 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N LYS A 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N GLU C 46 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N LYS A 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL C 48 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLY A 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N HIS C 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N VAL C 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 38 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N GLY E 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 40 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS E 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER C 42 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N LYS E 45 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 9.343A pdb=" N THR C 44 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY E 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLU C 46 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N VAL C 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 10.300A pdb=" N GLY E 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N HIS C 50 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N THR E 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL C 52 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL E 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N THR C 54 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU E 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLY G 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL E 48 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL G 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS E 50 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY G 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.350A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N ASN C 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLN E 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ASN G 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N THR E 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 79 removed outlier: 9.051A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA C 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL C 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 79 removed outlier: 9.051A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N THR C 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL A 71 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL C 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N GLY A 73 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA C 76 " --> pdb=" O GLY A 73 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N THR A 75 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ALA C 78 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL A 77 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA E 76 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR C 75 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N ALA E 78 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR E 75 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ALA G 78 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL E 77 " --> pdb=" O ALA G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 85 through 90 removed outlier: 6.474A pdb=" N ALA E 85 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N ILE G 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N SER E 87 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N ALA G 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA E 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 16 through 21 removed outlier: 6.360A pdb=" N ALA D 17 " --> pdb=" O ALA F 18 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU F 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA D 19 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 37 through 55 removed outlier: 6.332A pdb=" N LEU B 38 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLY D 41 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 40 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N LYS D 43 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N SER B 42 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N LYS D 45 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 9.349A pdb=" N THR B 44 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N GLY D 47 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.162A pdb=" N GLU B 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 10.180A pdb=" N VAL D 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N VAL B 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.314A pdb=" N GLY D 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS B 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR D 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 52 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N VAL D 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR B 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N VAL D 37 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 10.097A pdb=" N VAL F 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 9.191A pdb=" N TYR D 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N SER F 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N GLY D 41 " --> pdb=" O SER F 42 " (cutoff:3.500A) removed outlier: 10.118A pdb=" N THR F 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N LYS D 43 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 9.862A pdb=" N GLU F 46 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS D 45 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N VAL F 48 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLY D 47 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N HIS F 50 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL D 49 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N VAL F 52 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N GLY D 51 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 9.865A pdb=" N THR F 54 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N THR D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLU F 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY H 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL F 48 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL H 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N HIS F 50 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLY H 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 66 removed outlier: 6.260A pdb=" N GLN B 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASN D 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N THR B 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN D 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ASN F 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR D 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLN F 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN H 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 69 through 79 removed outlier: 9.040A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N THR D 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL B 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N VAL D 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY B 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 76 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 69 through 79 removed outlier: 9.040A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N THR D 72 " --> pdb=" O ALA B 69 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N VAL B 71 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N VAL D 74 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N GLY B 73 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 76 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N THR B 75 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ALA D 78 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL B 77 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA F 76 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N THR D 75 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ALA F 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL D 77 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 85 through 90 removed outlier: 6.443A pdb=" N ALA B 85 " --> pdb=" O GLY D 86 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE D 88 " --> pdb=" O ALA B 85 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER B 87 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALA D 90 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA B 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA F 85 " --> pdb=" O GLY H 86 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ILE H 88 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER F 87 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ALA H 90 " --> pdb=" O SER F 87 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA F 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) 65 hydrogen bonds defined for protein. 195 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: 0.50 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 624 1.29 - 1.35: 548 1.35 - 1.42: 91 1.42 - 1.48: 604 1.48 - 1.55: 1661 Bond restraints: 3528 Sorted by residual: bond pdb=" C THR G 81 " pdb=" N VAL G 82 " ideal model delta sigma weight residual 1.332 1.425 -0.093 1.36e-02 5.41e+03 4.65e+01 bond pdb=" C THR H 81 " pdb=" N VAL H 82 " ideal model delta sigma weight residual 1.332 1.393 -0.061 1.36e-02 5.41e+03 2.01e+01 bond pdb=" C VAL G 82 " pdb=" N GLU G 83 " ideal model delta sigma weight residual 1.336 1.381 -0.045 1.55e-02 4.16e+03 8.46e+00 bond pdb=" N GLU D 61 " pdb=" CA GLU D 61 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.20e+00 bond pdb=" C VAL H 82 " pdb=" N GLU H 83 " ideal model delta sigma weight residual 1.334 1.368 -0.034 1.39e-02 5.18e+03 5.97e+00 ... (remaining 3523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.80: 4229 0.80 - 1.60: 430 1.60 - 2.40: 94 2.40 - 3.20: 17 3.20 - 4.01: 14 Bond angle restraints: 4784 Sorted by residual: angle pdb=" C LYS H 60 " pdb=" N GLU H 61 " pdb=" CA GLU H 61 " ideal model delta sigma weight residual 122.73 118.88 3.85 1.62e+00 3.81e-01 5.66e+00 angle pdb=" C LYS F 60 " pdb=" N GLU F 61 " pdb=" CA GLU F 61 " ideal model delta sigma weight residual 122.73 119.02 3.71 1.62e+00 3.81e-01 5.25e+00 angle pdb=" C LYS D 60 " pdb=" N GLU D 61 " pdb=" CA GLU D 61 " ideal model delta sigma weight residual 122.62 119.06 3.56 1.56e+00 4.11e-01 5.20e+00 angle pdb=" C LYS E 60 " pdb=" N GLU E 61 " pdb=" CA GLU E 61 " ideal model delta sigma weight residual 122.73 119.10 3.63 1.62e+00 3.81e-01 5.02e+00 angle pdb=" C VAL G 82 " pdb=" N GLU G 83 " pdb=" CA GLU G 83 " ideal model delta sigma weight residual 122.14 125.85 -3.71 1.67e+00 3.59e-01 4.92e+00 ... (remaining 4779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.25: 1936 10.25 - 20.50: 88 20.50 - 30.75: 19 30.75 - 41.00: 13 41.00 - 51.24: 8 Dihedral angle restraints: 2064 sinusoidal: 656 harmonic: 1408 Sorted by residual: dihedral pdb=" CA VAL G 74 " pdb=" C VAL G 74 " pdb=" N THR G 75 " pdb=" CA THR G 75 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.76e+00 dihedral pdb=" CA VAL F 74 " pdb=" C VAL F 74 " pdb=" N THR F 75 " pdb=" CA THR F 75 " ideal model delta harmonic sigma weight residual 180.00 164.55 15.45 0 5.00e+00 4.00e-02 9.55e+00 dihedral pdb=" N LYS B 43 " pdb=" CA LYS B 43 " pdb=" CB LYS B 43 " pdb=" CG LYS B 43 " ideal model delta sinusoidal sigma weight residual -60.00 -111.24 51.24 3 1.50e+01 4.44e-03 8.99e+00 ... (remaining 2061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 282 0.026 - 0.052: 199 0.052 - 0.077: 78 0.077 - 0.103: 49 0.103 - 0.129: 56 Chirality restraints: 664 Sorted by residual: chirality pdb=" CA ILE D 88 " pdb=" N ILE D 88 " pdb=" C ILE D 88 " pdb=" CB ILE D 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01 ... (remaining 661 not shown) Planarity restraints: 584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS H 60 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.49e+00 pdb=" C LYS H 60 " -0.027 2.00e-02 2.50e+03 pdb=" O LYS H 60 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU H 61 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 60 " -0.007 2.00e-02 2.50e+03 1.50e-02 2.26e+00 pdb=" C LYS E 60 " 0.026 2.00e-02 2.50e+03 pdb=" O LYS E 60 " -0.010 2.00e-02 2.50e+03 pdb=" N GLU E 61 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 60 " 0.007 2.00e-02 2.50e+03 1.39e-02 1.92e+00 pdb=" C LYS F 60 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS F 60 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU F 61 " 0.008 2.00e-02 2.50e+03 ... (remaining 581 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 130 2.74 - 3.28: 3097 3.28 - 3.82: 5556 3.82 - 4.36: 6647 4.36 - 4.90: 12606 Nonbonded interactions: 28036 Sorted by model distance: nonbonded pdb=" NZ LYS A 45 " pdb=" OE2 GLU B 46 " model vdw 2.202 3.120 nonbonded pdb=" NZ LYS C 45 " pdb=" OE2 GLU D 46 " model vdw 2.208 3.120 nonbonded pdb=" OE1 GLU C 61 " pdb=" OG1 THR C 92 " model vdw 2.209 3.040 nonbonded pdb=" NZ LYS G 45 " pdb=" OE2 GLU H 46 " model vdw 2.210 3.120 nonbonded pdb=" NZ LYS E 45 " pdb=" OE2 GLU F 46 " model vdw 2.218 3.120 ... (remaining 28031 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' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.720 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.560 Find NCS groups from input model: 0.060 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 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 : 0.004 0.093 3528 Z= 0.237 Angle : 0.580 4.005 4784 Z= 0.345 Chirality : 0.052 0.129 664 Planarity : 0.002 0.016 584 Dihedral : 8.602 51.243 1168 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.30), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.005 TYR E 39 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 3528) covalent geometry : angle 0.57998 ( 4784) hydrogen bonds : bond 0.15124 ( 65) hydrogen bonds : angle 7.15443 ( 195) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.139 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 0.5514 time to fit residues: 70.3959 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN E 79 GLN F 65 ASN G 65 ASN G 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.154596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.141332 restraints weight = 3571.650| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.40 r_work: 0.3920 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3528 Z= 0.244 Angle : 0.578 5.403 4784 Z= 0.327 Chirality : 0.053 0.132 664 Planarity : 0.003 0.010 584 Dihedral : 6.022 16.345 512 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.51 % Favored : 95.08 % Rotamer: Outliers : 4.17 % Allowed : 10.83 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.07 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR H 39 HIS 0.004 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00517 ( 3528) covalent geometry : angle 0.57848 ( 4784) hydrogen bonds : bond 0.03334 ( 65) hydrogen bonds : angle 5.84478 ( 195) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.151 Fit side-chains REVERT: B 46 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: C 45 LYS cc_start: 0.9093 (tttt) cc_final: 0.8831 (tttp) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.5375 time to fit residues: 53.0793 Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 43 optimal weight: 0.0970 chunk 47 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.154427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141300 restraints weight = 3566.793| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.40 r_work: 0.3917 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.3835 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3528 Z= 0.210 Angle : 0.546 5.016 4784 Z= 0.306 Chirality : 0.052 0.131 664 Planarity : 0.002 0.007 584 Dihedral : 5.822 16.341 512 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.66 % Favored : 96.93 % Rotamer: Outliers : 2.78 % Allowed : 11.39 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR A 39 HIS 0.003 0.002 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 3528) covalent geometry : angle 0.54614 ( 4784) hydrogen bonds : bond 0.02620 ( 65) hydrogen bonds : angle 5.56996 ( 195) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.138 Fit side-chains REVERT: B 46 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: C 45 LYS cc_start: 0.9089 (tttt) cc_final: 0.8828 (tttp) outliers start: 10 outliers final: 8 residues processed: 92 average time/residue: 0.5618 time to fit residues: 53.1323 Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.152488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.139641 restraints weight = 3588.647| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.35 r_work: 0.3903 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 3528 Z= 0.283 Angle : 0.617 5.289 4784 Z= 0.347 Chirality : 0.054 0.133 664 Planarity : 0.003 0.008 584 Dihedral : 6.208 16.758 512 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.71 % Favored : 94.67 % Rotamer: Outliers : 4.44 % Allowed : 13.06 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.002 TYR H 39 HIS 0.003 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00596 ( 3528) covalent geometry : angle 0.61712 ( 4784) hydrogen bonds : bond 0.02991 ( 65) hydrogen bonds : angle 5.72535 ( 195) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.102 Fit side-chains REVERT: B 46 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: B 83 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7608 (mt-10) REVERT: C 45 LYS cc_start: 0.9093 (tttt) cc_final: 0.8841 (tttp) REVERT: E 43 LYS cc_start: 0.8567 (mtpm) cc_final: 0.8248 (tttm) REVERT: H 43 LYS cc_start: 0.8301 (mtpm) cc_final: 0.8003 (mttp) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.5002 time to fit residues: 47.3595 Evaluate side-chains 97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.153530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.140684 restraints weight = 3578.515| |-----------------------------------------------------------------------------| r_work (start): 0.3981 rms_B_bonded: 1.37 r_work: 0.3913 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3528 Z= 0.225 Angle : 0.561 5.112 4784 Z= 0.314 Chirality : 0.052 0.132 664 Planarity : 0.002 0.006 584 Dihedral : 5.897 16.820 512 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.28 % Favored : 96.31 % Rotamer: Outliers : 5.56 % Allowed : 14.17 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 3528) covalent geometry : angle 0.56085 ( 4784) hydrogen bonds : bond 0.02510 ( 65) hydrogen bonds : angle 5.54561 ( 195) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.140 Fit side-chains REVERT: B 46 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: C 45 LYS cc_start: 0.9072 (tttt) cc_final: 0.8828 (tttp) REVERT: H 43 LYS cc_start: 0.8288 (mtpm) cc_final: 0.7973 (mttp) outliers start: 20 outliers final: 17 residues processed: 98 average time/residue: 0.4981 time to fit residues: 50.3209 Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 18 optimal weight: 6.9990 chunk 11 optimal weight: 0.0980 chunk 12 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.154369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.141553 restraints weight = 3584.049| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.37 r_work: 0.3924 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3843 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3528 Z= 0.189 Angle : 0.532 5.446 4784 Z= 0.297 Chirality : 0.051 0.130 664 Planarity : 0.002 0.007 584 Dihedral : 5.684 16.920 512 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 5.00 % Allowed : 15.28 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.16 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.002 TYR F 39 HIS 0.002 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 3528) covalent geometry : angle 0.53151 ( 4784) hydrogen bonds : bond 0.02218 ( 65) hydrogen bonds : angle 5.41220 ( 195) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.194 Fit side-chains REVERT: B 46 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: C 45 LYS cc_start: 0.9074 (tttt) cc_final: 0.8830 (tttp) REVERT: E 43 LYS cc_start: 0.8558 (mtpm) cc_final: 0.8254 (tttm) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.5904 time to fit residues: 58.9144 Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 41 optimal weight: 8.9990 chunk 40 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.151916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.139106 restraints weight = 3620.882| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.35 r_work: 0.3890 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 3528 Z= 0.325 Angle : 0.660 5.771 4784 Z= 0.370 Chirality : 0.056 0.137 664 Planarity : 0.003 0.009 584 Dihedral : 6.357 17.645 512 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.61 % Allowed : 5.12 % Favored : 94.26 % Rotamer: Outliers : 5.56 % Allowed : 15.83 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.017 0.003 TYR G 39 HIS 0.004 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00687 ( 3528) covalent geometry : angle 0.65975 ( 4784) hydrogen bonds : bond 0.03140 ( 65) hydrogen bonds : angle 5.79253 ( 195) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.132 Fit side-chains REVERT: B 46 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: C 43 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8183 (tttt) REVERT: C 45 LYS cc_start: 0.9080 (tttt) cc_final: 0.8838 (tttp) REVERT: H 43 LYS cc_start: 0.8349 (mtpm) cc_final: 0.8038 (mttp) outliers start: 20 outliers final: 18 residues processed: 100 average time/residue: 0.5368 time to fit residues: 55.2162 Evaluate side-chains 107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 39 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 0.2980 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 0.2980 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.154840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.142065 restraints weight = 3619.472| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 1.37 r_work: 0.3929 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3528 Z= 0.165 Angle : 0.527 5.728 4784 Z= 0.290 Chirality : 0.051 0.131 664 Planarity : 0.002 0.007 584 Dihedral : 5.590 16.828 512 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.87 % Favored : 96.93 % Rotamer: Outliers : 5.28 % Allowed : 16.39 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.17 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.002 TYR F 39 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 3528) covalent geometry : angle 0.52706 ( 4784) hydrogen bonds : bond 0.02071 ( 65) hydrogen bonds : angle 5.33534 ( 195) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.136 Fit side-chains REVERT: B 46 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: C 45 LYS cc_start: 0.9056 (tttt) cc_final: 0.8815 (tttp) REVERT: E 43 LYS cc_start: 0.8562 (mtpm) cc_final: 0.8258 (tttm) outliers start: 19 outliers final: 18 residues processed: 100 average time/residue: 0.5240 time to fit residues: 53.9819 Evaluate side-chains 107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 43 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.150279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.137407 restraints weight = 3625.050| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 1.35 r_work: 0.3869 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.058 3528 Z= 0.471 Angle : 0.792 6.374 4784 Z= 0.447 Chirality : 0.063 0.157 664 Planarity : 0.004 0.013 584 Dihedral : 6.811 18.723 512 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.82 % Allowed : 5.94 % Favored : 93.24 % Rotamer: Outliers : 6.11 % Allowed : 15.83 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.13 (0.28), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR H 39 HIS 0.005 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00999 ( 3528) covalent geometry : angle 0.79242 ( 4784) hydrogen bonds : bond 0.03914 ( 65) hydrogen bonds : angle 6.14017 ( 195) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.141 Fit side-chains REVERT: C 43 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8192 (tttt) REVERT: C 45 LYS cc_start: 0.9088 (tttt) cc_final: 0.8854 (tttp) outliers start: 22 outliers final: 17 residues processed: 102 average time/residue: 0.5574 time to fit residues: 58.5380 Evaluate side-chains 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.155527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.142712 restraints weight = 3659.557| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.38 r_work: 0.3940 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3528 Z= 0.145 Angle : 0.522 6.503 4784 Z= 0.285 Chirality : 0.051 0.130 664 Planarity : 0.002 0.007 584 Dihedral : 5.479 16.902 512 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.66 % Favored : 97.13 % Rotamer: Outliers : 4.72 % Allowed : 17.78 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.19 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.42 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.001 TYR H 39 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3528) covalent geometry : angle 0.52183 ( 4784) hydrogen bonds : bond 0.01895 ( 65) hydrogen bonds : angle 5.29224 ( 195) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.143 Fit side-chains REVERT: C 45 LYS cc_start: 0.9054 (tttt) cc_final: 0.8821 (tttp) REVERT: E 43 LYS cc_start: 0.8521 (mtpm) cc_final: 0.8205 (tttm) outliers start: 17 outliers final: 17 residues processed: 98 average time/residue: 0.5483 time to fit residues: 55.3886 Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 42 SER Chi-restraints excluded: chain H residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 0.0370 chunk 28 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.153178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140308 restraints weight = 3610.616| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.35 r_work: 0.3910 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3830 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3528 Z= 0.230 Angle : 0.589 6.654 4784 Z= 0.326 Chirality : 0.052 0.134 664 Planarity : 0.002 0.008 584 Dihedral : 5.953 17.336 512 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.92 % Favored : 94.88 % Rotamer: Outliers : 5.00 % Allowed : 17.50 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.002 TYR H 39 HIS 0.003 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 3528) covalent geometry : angle 0.58860 ( 4784) hydrogen bonds : bond 0.02501 ( 65) hydrogen bonds : angle 5.53146 ( 195) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.75 seconds wall clock time: 31 minutes 54.52 seconds (1914.52 seconds total)