Starting phenix.real_space_refine on Wed Jul 23 14:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ckk_45650/07_2025/9ckk_45650.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ckk_45650/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ckk_45650/07_2025/9ckk_45650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ckk_45650/07_2025/9ckk_45650.map" model { file = "/net/cci-nas-00/data/ceres_data/9ckk_45650/07_2025/9ckk_45650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ckk_45650/07_2025/9ckk_45650.cif" } resolution = 2.21 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= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.16, per 1000 atoms: 0.90 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: 0.80 Conformation dependent library (CDL) restraints added in 476.1 milliseconds 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: 0.54 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: 0.93 Time building geometry restraints manager: 0.97 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: 0.01 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: 2.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.290 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 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:13.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.030 ------------------------------------------------------------------------------- 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 (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: -3.05 (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 HIS 0.002 0.001 HIS B 50 TYR 0.020 0.005 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.15124 ( 65) hydrogen bonds : angle 7.15443 ( 195) covalent geometry : bond 0.00436 ( 3528) covalent geometry : angle 0.57998 ( 4784) *********************** 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 : 0.379 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 124 average time/residue: 1.1089 time to fit residues: 141.5650 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 : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.4145 r_free = 0.4145 target = 0.154478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141277 restraints weight = 3528.774| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 1.38 r_work: 0.3920 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3838 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1662 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= 0.251 Angle : 0.587 5.464 4784 Z= 0.332 Chirality : 0.054 0.133 664 Planarity : 0.003 0.010 584 Dihedral : 6.060 16.368 512 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.64 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 (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: -3.08 (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 HIS 0.004 0.002 HIS F 50 TYR 0.009 0.002 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.03349 ( 65) hydrogen bonds : angle 5.85520 ( 195) covalent geometry : bond 0.00532 ( 3528) covalent geometry : angle 0.58675 ( 4784) *********************** 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 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.363 Fit side-chains REVERT: B 46 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: C 45 LYS cc_start: 0.9094 (tttt) cc_final: 0.8831 (tttp) outliers start: 15 outliers final: 8 residues processed: 97 average time/residue: 1.0906 time to fit residues: 109.0622 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 : 0.379 ------------------------------------------------------------------------------- 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 41 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 9 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.151145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.138074 restraints weight = 3624.634| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.37 r_work: 0.3880 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3801 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 3528 Z= 0.402 Angle : 0.731 5.091 4784 Z= 0.413 Chirality : 0.060 0.140 664 Planarity : 0.003 0.012 584 Dihedral : 6.683 17.657 512 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 1.02 % Allowed : 5.33 % Favored : 93.65 % Rotamer: Outliers : 5.00 % Allowed : 11.11 % Favored : 83.89 % 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: -3.10 (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 HIS 0.005 0.003 HIS H 50 TYR 0.012 0.003 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 65) hydrogen bonds : angle 6.08033 ( 195) covalent geometry : bond 0.00849 ( 3528) covalent geometry : angle 0.73105 ( 4784) *********************** 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 107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.374 Fit side-chains REVERT: C 45 LYS cc_start: 0.9112 (tttt) cc_final: 0.8858 (tttp) outliers start: 18 outliers final: 14 residues processed: 96 average time/residue: 1.1961 time to fit residues: 118.0391 Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 D residue 15 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 16 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.4144 r_free = 0.4144 target = 0.154885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142090 restraints weight = 3543.407| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 1.37 r_work: 0.3928 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3847 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3528 Z= 0.175 Angle : 0.528 6.141 4784 Z= 0.294 Chirality : 0.051 0.130 664 Planarity : 0.002 0.007 584 Dihedral : 5.702 16.717 512 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.41 % Allowed : 2.66 % Favored : 96.93 % Rotamer: Outliers : 3.33 % Allowed : 15.00 % Favored : 81.67 % 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: -3.14 (0.29), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.22), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 TYR 0.014 0.002 TYR A 39 Details of bonding type rmsd hydrogen bonds : bond 0.02259 ( 65) hydrogen bonds : angle 5.51170 ( 195) covalent geometry : bond 0.00360 ( 3528) covalent geometry : angle 0.52848 ( 4784) *********************** 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 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.400 Fit side-chains REVERT: C 45 LYS cc_start: 0.9062 (tttt) cc_final: 0.8824 (tttp) REVERT: E 43 LYS cc_start: 0.8556 (mtpm) cc_final: 0.8253 (tttm) REVERT: H 43 LYS cc_start: 0.8371 (mtpm) cc_final: 0.8021 (mttp) outliers start: 12 outliers final: 9 residues processed: 91 average time/residue: 1.1437 time to fit residues: 107.2019 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 : 0.413 ------------------------------------------------------------------------------- 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 16 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain E residue 92 THR 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 17 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 44 optimal weight: 0.0970 chunk 27 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 2 optimal weight: 0.0040 chunk 42 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 overall best weight: 1.5792 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.154123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.141229 restraints weight = 3623.237| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.38 r_work: 0.3919 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.3837 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3528 Z= 0.191 Angle : 0.536 5.450 4784 Z= 0.299 Chirality : 0.051 0.132 664 Planarity : 0.002 0.007 584 Dihedral : 5.738 16.772 512 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.30 % Favored : 95.49 % Rotamer: Outliers : 5.00 % Allowed : 14.72 % 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 (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: -3.13 (0.30), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 TYR 0.012 0.002 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.02321 ( 65) hydrogen bonds : angle 5.47795 ( 195) covalent geometry : bond 0.00396 ( 3528) covalent geometry : angle 0.53593 ( 4784) *********************** 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 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 0.402 Fit side-chains REVERT: C 45 LYS cc_start: 0.9076 (tttt) cc_final: 0.8824 (tttp) REVERT: E 43 LYS cc_start: 0.8553 (mtpm) cc_final: 0.8256 (tttm) outliers start: 18 outliers final: 16 residues processed: 94 average time/residue: 1.0821 time to fit residues: 104.9561 Evaluate side-chains 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.450 ------------------------------------------------------------------------------- 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 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 16 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 0.0670 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.8126 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.152019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.139189 restraints weight = 3662.304| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 1.36 r_work: 0.3891 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3811 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 3528 Z= 0.307 Angle : 0.642 5.655 4784 Z= 0.361 Chirality : 0.055 0.136 664 Planarity : 0.003 0.009 584 Dihedral : 6.317 17.485 512 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.33 % Favored : 94.26 % Rotamer: Outliers : 5.83 % Allowed : 13.89 % 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 (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: -3.11 (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 HIS 0.004 0.002 HIS H 50 TYR 0.015 0.003 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 65) hydrogen bonds : angle 5.80277 ( 195) covalent geometry : bond 0.00650 ( 3528) covalent geometry : angle 0.64227 ( 4784) *********************** 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 109 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.380 Fit side-chains REVERT: C 43 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8179 (tttt) REVERT: C 45 LYS cc_start: 0.9075 (tttt) cc_final: 0.8833 (tttp) outliers start: 21 outliers final: 17 residues processed: 100 average time/residue: 1.0612 time to fit residues: 109.4560 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 : 0.403 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 10 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4139 r_free = 0.4139 target = 0.154371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.141572 restraints weight = 3554.571| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.36 r_work: 0.3922 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3841 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2087 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= 0.185 Angle : 0.542 5.855 4784 Z= 0.299 Chirality : 0.051 0.131 664 Planarity : 0.002 0.007 584 Dihedral : 5.729 16.891 512 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.28 % Favored : 96.52 % Rotamer: Outliers : 5.28 % Allowed : 15.83 % Favored : 78.89 % 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: -3.14 (0.30), residues: 488 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.23), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 50 TYR 0.013 0.002 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02202 ( 65) hydrogen bonds : angle 5.44716 ( 195) covalent geometry : bond 0.00384 ( 3528) covalent geometry : angle 0.54165 ( 4784) *********************** 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 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.393 Fit side-chains REVERT: C 45 LYS cc_start: 0.9060 (tttt) cc_final: 0.8816 (tttp) REVERT: E 43 LYS cc_start: 0.8560 (mtpm) cc_final: 0.8243 (tttm) outliers start: 19 outliers final: 19 residues processed: 99 average time/residue: 0.9920 time to fit residues: 101.4267 Evaluate side-chains 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 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 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 13 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 = 0.4112 r_free = 0.4112 target = 0.152254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.139347 restraints weight = 3647.674| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 1.36 r_work: 0.3894 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3528 Z= 0.280 Angle : 0.627 6.404 4784 Z= 0.349 Chirality : 0.054 0.135 664 Planarity : 0.002 0.008 584 Dihedral : 6.205 17.362 512 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.12 % Favored : 94.67 % Rotamer: Outliers : 5.56 % Allowed : 16.94 % 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 (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: -3.10 (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 HIS 0.003 0.001 HIS G 50 TYR 0.015 0.003 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02846 ( 65) hydrogen bonds : angle 5.71590 ( 195) covalent geometry : bond 0.00590 ( 3528) covalent geometry : angle 0.62711 ( 4784) *********************** 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 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.380 Fit side-chains REVERT: C 43 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8177 (tttt) REVERT: C 45 LYS cc_start: 0.9075 (tttt) cc_final: 0.8833 (tttp) REVERT: E 43 LYS cc_start: 0.8563 (mtpm) cc_final: 0.8242 (tttm) outliers start: 20 outliers final: 18 residues processed: 97 average time/residue: 1.0500 time to fit residues: 105.0996 Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 31 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.152173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.139368 restraints weight = 3531.974| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 1.34 r_work: 0.3893 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3528 Z= 0.304 Angle : 0.650 6.382 4784 Z= 0.362 Chirality : 0.055 0.135 664 Planarity : 0.003 0.009 584 Dihedral : 6.296 17.502 512 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.10 % Favored : 95.29 % Rotamer: Outliers : 5.56 % Allowed : 17.22 % Favored : 77.22 % 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: -3.11 (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 HIS 0.003 0.001 HIS H 50 TYR 0.018 0.003 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02997 ( 65) hydrogen bonds : angle 5.78898 ( 195) covalent geometry : bond 0.00640 ( 3528) covalent geometry : angle 0.64988 ( 4784) *********************** 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 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.372 Fit side-chains REVERT: C 43 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8182 (tttt) REVERT: C 45 LYS cc_start: 0.9077 (tttt) cc_final: 0.8837 (tttp) REVERT: E 43 LYS cc_start: 0.8574 (mtpm) cc_final: 0.8248 (tttm) outliers start: 20 outliers final: 18 residues processed: 97 average time/residue: 1.0528 time to fit residues: 105.3602 Evaluate side-chains 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.152614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.139761 restraints weight = 3580.969| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.35 r_work: 0.3897 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3818 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3528 Z= 0.266 Angle : 0.617 6.502 4784 Z= 0.343 Chirality : 0.054 0.134 664 Planarity : 0.002 0.008 584 Dihedral : 6.185 17.537 512 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.61 % Allowed : 4.51 % Favored : 94.88 % Rotamer: Outliers : 5.56 % Allowed : 17.22 % Favored : 77.22 % 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: -3.12 (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 HIS 0.003 0.001 HIS G 50 TYR 0.017 0.003 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02737 ( 65) hydrogen bonds : angle 5.72094 ( 195) covalent geometry : bond 0.00558 ( 3528) covalent geometry : angle 0.61700 ( 4784) ********************** 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 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.399 Fit side-chains REVERT: C 43 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8175 (tttt) REVERT: C 45 LYS cc_start: 0.9072 (tttt) cc_final: 0.8831 (tttp) REVERT: E 43 LYS cc_start: 0.8574 (mtpm) cc_final: 0.8243 (tttm) outliers start: 20 outliers final: 19 residues processed: 97 average time/residue: 1.0173 time to fit residues: 101.9073 Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 92 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.4122 r_free = 0.4122 target = 0.153086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.140236 restraints weight = 3606.377| |-----------------------------------------------------------------------------| r_work (start): 0.3972 rms_B_bonded: 1.35 r_work: 0.3905 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2179 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 : 0.600 6.659 4784 Z= 0.333 Chirality : 0.053 0.133 664 Planarity : 0.002 0.007 584 Dihedral : 6.090 17.387 512 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.10 % Favored : 95.70 % Rotamer: Outliers : 5.56 % Allowed : 17.22 % Favored : 77.22 % 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: -3.13 (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 HIS 0.003 0.001 HIS G 50 TYR 0.017 0.003 TYR F 39 Details of bonding type rmsd hydrogen bonds : bond 0.02601 ( 65) hydrogen bonds : angle 5.66169 ( 195) covalent geometry : bond 0.00509 ( 3528) covalent geometry : angle 0.60010 ( 4784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3539.04 seconds wall clock time: 60 minutes 55.47 seconds (3655.47 seconds total)