Starting phenix.real_space_refine on Fri Sep 11 02:51:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.cif Found real_map, /net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6l1t_0801/09_2026/6l1t_0801.map" } resolution = 3.22 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= 0.004 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 10 5.16 5 C 4360 2.51 5 N 1210 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7010 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 701 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PTR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.82, per 1000 atoms: 0.12 Number of scatterers: 7010 At special positions: 0 Unit cell: (194.743, 91.49, 50.973, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 10 15.00 O 1420 8.00 N 1210 7.00 C 4360 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: 0.44 Conformation dependent library (CDL) restraints added in 383.1 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1720 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 25 sheets defined 0.0% alpha, 45.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 removed outlier: 6.243A pdb=" N PHE A 4 " --> pdb=" O MET B 5 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N GLY B 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS A 6 " --> pdb=" O GLY B 7 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE B 4 " --> pdb=" O MET C 5 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N GLY C 7 " --> pdb=" O PHE B 4 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS B 6 " --> pdb=" O GLY C 7 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N PHE C 4 " --> pdb=" O MET D 5 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N GLY D 7 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS C 6 " --> pdb=" O GLY D 7 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE D 4 " --> pdb=" O MET E 5 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY E 7 " --> pdb=" O PHE D 4 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LYS D 6 " --> pdb=" O GLY E 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.921A pdb=" N LYS A 10 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS B 10 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS C 10 " --> pdb=" O ALA D 11 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS D 10 " --> pdb=" O ALA E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 16 removed outlier: 6.639A pdb=" N VAL A 15 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 15 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL C 15 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ALA D 18 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL E 15 " --> pdb=" O GLY D 14 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 16 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ALA E 17 " --> pdb=" O VAL D 16 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.938A pdb=" N VAL A 26 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL B 26 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL C 26 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL D 26 " --> pdb=" O ALA E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 36 removed outlier: 5.387A pdb=" N GLU A 35 " --> pdb=" O GLY B 36 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N GLY B 31 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 10.595A pdb=" N LYS C 34 " --> pdb=" O GLY B 31 " (cutoff:3.500A) removed outlier: 9.255A pdb=" N THR B 33 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N GLY C 36 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N GLU B 35 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLY C 31 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 10.597A pdb=" N LYS D 34 " --> pdb=" O GLY C 31 " (cutoff:3.500A) removed outlier: 9.246A pdb=" N THR C 33 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 9.328A pdb=" N GLY D 36 " --> pdb=" O THR C 33 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU C 35 " --> pdb=" O GLY D 36 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N GLY D 31 " --> pdb=" O LYS E 32 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N LYS E 34 " --> pdb=" O GLY D 31 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N THR D 33 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N GLY E 36 " --> pdb=" O THR D 33 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU D 35 " --> pdb=" O GLY E 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 39 through 40 removed outlier: 6.269A pdb=" N PTR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PTR B 39 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PTR C 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N PTR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 43 through 45 removed outlier: 6.588A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS B 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LYS C 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 48 through 49 removed outlier: 6.374A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL D 48 " --> pdb=" O VAL E 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 52 through 54 removed outlier: 6.621A pdb=" N ALA A 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA C 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA D 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 70 through 82 removed outlier: 6.949A pdb=" N VAL A 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA A 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA B 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN C 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR D 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA C 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL D 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA C 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN D 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS C 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR D 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 70 through 82 removed outlier: 6.949A pdb=" N VAL A 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR B 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ALA A 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 77 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA A 78 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLN B 79 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LYS A 80 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N THR B 81 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL A 82 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 74 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR C 75 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA B 76 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL C 77 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ALA B 78 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLN C 79 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS B 80 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR C 81 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B 82 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 74 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR D 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA C 76 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL D 77 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA C 78 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN D 79 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS C 80 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N THR D 81 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL C 82 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ALA E 78 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL D 77 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LYS E 80 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN D 79 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL E 82 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 81 " --> pdb=" O VAL E 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 89 through 96 removed outlier: 8.887A pdb=" N ALA A 89 " --> pdb=" O ALA B 90 " (cutoff:3.500A) removed outlier: 10.093A pdb=" N THR B 92 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 8.863A pdb=" N ALA A 91 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 10.089A pdb=" N PHE B 94 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLY A 93 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N LYS B 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 95 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N ALA B 89 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 10.121A pdb=" N THR C 92 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ALA B 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N PHE C 94 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLY B 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N LYS C 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N ALA C 89 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 10.076A pdb=" N THR D 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N ALA C 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N PHE D 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY C 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N LYS D 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL C 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N ALA D 89 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 9.917A pdb=" N THR E 92 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ALA D 91 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 9.844A pdb=" N PHE E 94 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLY D 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N LYS E 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL D 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 4 through 7 removed outlier: 6.224A pdb=" N PHE F 4 " --> pdb=" O MET G 5 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLY G 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS F 6 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE G 4 " --> pdb=" O MET H 5 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N GLY H 7 " --> pdb=" O PHE G 4 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LYS G 6 " --> pdb=" O GLY H 7 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE H 4 " --> pdb=" O MET I 5 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N GLY I 7 " --> pdb=" O PHE H 4 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LYS H 6 " --> pdb=" O GLY I 7 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE I 4 " --> pdb=" O MET J 5 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY J 7 " --> pdb=" O PHE I 4 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N LYS I 6 " --> pdb=" O GLY J 7 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.880A pdb=" N LYS F 10 " --> pdb=" O ALA G 11 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS G 10 " --> pdb=" O ALA H 11 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS H 10 " --> pdb=" O ALA I 11 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS I 10 " --> pdb=" O ALA J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 14 through 16 removed outlier: 6.713A pdb=" N VAL F 15 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL G 15 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL H 15 " --> pdb=" O VAL I 16 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA I 18 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N ALA J 17 " --> pdb=" O VAL I 16 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 26 through 28 removed outlier: 7.025A pdb=" N VAL F 26 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL G 26 " --> pdb=" O ALA H 27 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL H 26 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL I 26 " --> pdb=" O ALA J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 34 through 36 removed outlier: 5.470A pdb=" N GLU F 35 " --> pdb=" O GLY G 36 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N GLU G 35 " --> pdb=" O GLY H 36 " (cutoff:3.500A) removed outlier: 9.042A pdb=" N GLY H 31 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N LYS I 34 " --> pdb=" O GLY H 31 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N THR H 33 " --> pdb=" O LYS I 34 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N GLY I 36 " --> pdb=" O THR H 33 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU H 35 " --> pdb=" O GLY I 36 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS I 32 " --> pdb=" O THR J 33 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N GLU J 35 " --> pdb=" O LYS I 32 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N LYS I 34 " --> pdb=" O GLU J 35 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 39 through 40 removed outlier: 6.282A pdb=" N PTR F 39 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N PTR G 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PTR H 39 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N PTR I 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 43 through 45 removed outlier: 6.556A pdb=" N LYS F 43 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS G 43 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS H 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS I 43 " --> pdb=" O THR J 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 48 through 49 removed outlier: 6.402A pdb=" N VAL F 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL G 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL H 48 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL I 48 " --> pdb=" O VAL J 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.686A pdb=" N ALA F 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA G 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA H 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 70 through 82 removed outlier: 7.039A pdb=" N VAL F 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR G 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA F 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL G 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA F 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN G 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS F 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR G 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR H 75 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA G 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA G 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN H 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS G 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR H 81 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL G 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL H 74 " --> pdb=" O GLY I 73 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL I 74 " --> pdb=" O GLY J 73 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 70 through 82 removed outlier: 7.039A pdb=" N VAL F 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N THR G 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ALA F 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL G 77 " --> pdb=" O ALA F 76 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA F 78 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N GLN G 79 " --> pdb=" O ALA F 78 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LYS F 80 " --> pdb=" O GLN G 79 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR G 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 82 " --> pdb=" O THR G 81 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL G 74 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR H 75 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA G 76 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL H 77 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA G 78 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLN H 79 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS G 80 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR H 81 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL G 82 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ALA I 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL H 77 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS I 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN H 79 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N VAL I 82 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N THR H 81 " --> pdb=" O VAL I 82 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL I 77 " --> pdb=" O ALA J 78 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LYS J 80 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N GLN I 79 " --> pdb=" O LYS J 80 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL J 82 " --> pdb=" O GLN I 79 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR I 81 " --> pdb=" O VAL J 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.703A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL G 95 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL F 95 " --> pdb=" O LYS G 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 89 through 92 removed outlier: 6.703A pdb=" N ALA F 90 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLY G 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N THR F 92 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL G 95 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ALA G 89 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 10.055A pdb=" N THR H 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ALA G 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 10.032A pdb=" N PHE H 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLY G 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N LYS H 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL G 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA H 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 10.173A pdb=" N THR I 92 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ALA H 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 10.154A pdb=" N PHE I 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLY H 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N LYS I 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL H 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) removed outlier: 9.241A pdb=" N ALA I 89 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 10.496A pdb=" N THR J 92 " --> pdb=" O ALA I 89 " (cutoff:3.500A) removed outlier: 9.206A pdb=" N ALA I 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) removed outlier: 10.422A pdb=" N PHE J 94 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY I 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N LYS J 96 " --> pdb=" O GLY I 93 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL I 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 43 hydrogen bonds defined for protein. 129 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: 0.94 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2320 1.33 - 1.45: 517 1.45 - 1.57: 4173 1.57 - 1.68: 10 1.68 - 1.80: 20 Bond restraints: 7040 Sorted by residual: bond pdb=" OH PTR G 39 " pdb=" P PTR G 39 " ideal model delta sigma weight residual 1.769 1.604 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" OH PTR J 39 " pdb=" P PTR J 39 " ideal model delta sigma weight residual 1.769 1.604 0.165 2.00e-02 2.50e+03 6.77e+01 bond pdb=" OH PTR B 39 " pdb=" P PTR B 39 " ideal model delta sigma weight residual 1.769 1.605 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" OH PTR E 39 " pdb=" P PTR E 39 " ideal model delta sigma weight residual 1.769 1.605 0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" OH PTR D 39 " pdb=" P PTR D 39 " ideal model delta sigma weight residual 1.769 1.605 0.164 2.00e-02 2.50e+03 6.76e+01 ... (remaining 7035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 9118 1.96 - 3.92: 292 3.92 - 5.88: 36 5.88 - 7.83: 14 7.83 - 9.79: 10 Bond angle restraints: 9470 Sorted by residual: angle pdb=" OH PTR G 39 " pdb=" P PTR G 39 " pdb=" O2P PTR G 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.07e+01 angle pdb=" OH PTR F 39 " pdb=" P PTR F 39 " pdb=" O2P PTR F 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" OH PTR A 39 " pdb=" P PTR A 39 " pdb=" O2P PTR A 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" OH PTR D 39 " pdb=" P PTR D 39 " pdb=" O2P PTR D 39 " ideal model delta sigma weight residual 99.92 109.71 -9.79 3.00e+00 1.11e-01 1.06e+01 angle pdb=" OH PTR C 39 " pdb=" P PTR C 39 " pdb=" O2P PTR C 39 " ideal model delta sigma weight residual 99.92 109.69 -9.77 3.00e+00 1.11e-01 1.06e+01 ... (remaining 9465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.61: 3630 12.61 - 25.22: 390 25.22 - 37.83: 100 37.83 - 50.44: 40 50.44 - 63.05: 30 Dihedral angle restraints: 4190 sinusoidal: 1480 harmonic: 2710 Sorted by residual: dihedral pdb=" CA VAL B 49 " pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta harmonic sigma weight residual -180.00 -161.15 -18.85 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL G 49 " pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA VAL F 49 " pdb=" C VAL F 49 " pdb=" N HIS F 50 " pdb=" CA HIS F 50 " ideal model delta harmonic sigma weight residual -180.00 -161.17 -18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 578 0.035 - 0.071: 358 0.071 - 0.106: 132 0.106 - 0.142: 90 0.142 - 0.177: 22 Chirality restraints: 1180 Sorted by residual: chirality pdb=" CB VAL B 55 " pdb=" CA VAL B 55 " pdb=" CG1 VAL B 55 " pdb=" CG2 VAL B 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CB VAL J 55 " pdb=" CA VAL J 55 " pdb=" CG1 VAL J 55 " pdb=" CG2 VAL J 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.84e-01 chirality pdb=" CB VAL A 55 " pdb=" CA VAL A 55 " pdb=" CG1 VAL A 55 " pdb=" CG2 VAL A 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.77e-01 ... (remaining 1177 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 94 " -0.010 2.00e-02 2.50e+03 8.68e-03 1.32e+00 pdb=" CG PHE B 94 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE B 94 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 94 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 94 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 94 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 94 " 0.010 2.00e-02 2.50e+03 8.57e-03 1.29e+00 pdb=" CG PHE F 94 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE F 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE F 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 94 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 94 " 0.010 2.00e-02 2.50e+03 8.52e-03 1.27e+00 pdb=" CG PHE H 94 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE H 94 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE H 94 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE H 94 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE H 94 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2157 2.82 - 3.34: 5891 3.34 - 3.86: 10524 3.86 - 4.38: 11308 4.38 - 4.90: 22247 Nonbonded interactions: 52127 Sorted by model distance: nonbonded pdb=" NZ LYS D 34 " pdb=" O2P PTR E 39 " model vdw 2.296 3.120 nonbonded pdb=" NZ LYS G 34 " pdb=" O1P PTR G 39 " model vdw 2.314 3.120 nonbonded pdb=" NZ LYS D 34 " pdb=" O1P PTR D 39 " model vdw 2.314 3.120 nonbonded pdb=" NZ LYS E 34 " pdb=" O1P PTR E 39 " model vdw 2.314 3.120 nonbonded pdb=" NZ LYS F 34 " pdb=" O1P PTR F 39 " model vdw 2.314 3.120 ... (remaining 52122 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: 0.03 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' selection = chain 'I' selection = chain 'J' } 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: 2.860 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.760 Find NCS groups from input model: 0.070 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 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 : 0.011 0.165 7040 Z= 0.528 Angle : 0.919 9.793 9470 Z= 0.442 Chirality : 0.058 0.177 1180 Planarity : 0.002 0.009 1180 Dihedral : 14.062 63.051 2470 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % 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 are not related in a simple way. whole: -5.37 (0.15), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.08 (0.11), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.020 0.003 PHE B 94 HIS 0.006 0.004 HIS I 50 Details of bonding type rmsd/Z covalent geometry : bond 0.01133 / 0.53 ( 7040) covalent geometry : angle 0.91924 / 0.44 ( 9470) hydrogen bonds : bond 0.30207 / 21.14 ( 28) hydrogen bonds : angle 8.94177 / 5.60 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.168 Fit side-chains revert: symmetry clash REVERT: A 42 SER cc_start: 0.9172 (p) cc_final: 0.8949 (p) REVERT: E 32 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8281 (mtpp) REVERT: G 32 LYS cc_start: 0.8941 (ttpt) cc_final: 0.8520 (mtpp) REVERT: G 59 THR cc_start: 0.9161 (p) cc_final: 0.8923 (p) REVERT: I 2 ASP cc_start: 0.8725 (p0) cc_final: 0.8415 (p0) REVERT: J 57 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7065 (pm20) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.0589 time to fit residues: 16.0121 Evaluate side-chains 149 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.120807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107286 restraints weight = 10869.055| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.77 r_work: 0.3533 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7040 Z= 0.137 Angle : 0.594 7.225 9470 Z= 0.313 Chirality : 0.049 0.163 1180 Planarity : 0.002 0.014 1180 Dihedral : 6.367 38.058 1010 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 5.00 % Allowed : 18.38 % Favored : 76.62 % 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 are not related in a simple way. whole: -4.60 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE E 4 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7040) covalent geometry : angle 0.59436 / 0.31 ( 9470) hydrogen bonds : bond 0.04123 / 2.53 ( 28) hydrogen bonds : angle 5.04151 / 3.33 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 190 time to evaluate : 0.190 Fit side-chains REVERT: A 13 GLU cc_start: 0.7989 (tp30) cc_final: 0.7717 (tm-30) REVERT: A 42 SER cc_start: 0.9168 (p) cc_final: 0.8939 (p) REVERT: C 13 GLU cc_start: 0.8119 (tp30) cc_final: 0.7841 (tp30) REVERT: D 2 ASP cc_start: 0.8872 (p0) cc_final: 0.8537 (p0) REVERT: D 8 LEU cc_start: 0.9211 (mm) cc_final: 0.8817 (mm) REVERT: E 32 LYS cc_start: 0.8987 (ttpt) cc_final: 0.8536 (mtpt) REVERT: E 57 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7681 (mm-30) REVERT: E 83 GLU cc_start: 0.7570 (mp0) cc_final: 0.7214 (mp0) REVERT: G 13 GLU cc_start: 0.8251 (tp30) cc_final: 0.7152 (tp30) REVERT: G 32 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8495 (mtpp) REVERT: G 83 GLU cc_start: 0.7510 (mp0) cc_final: 0.7270 (mp0) REVERT: H 2 ASP cc_start: 0.8697 (p0) cc_final: 0.8397 (p0) REVERT: H 28 GLU cc_start: 0.7960 (tt0) cc_final: 0.7646 (mt-10) REVERT: J 2 ASP cc_start: 0.8554 (p0) cc_final: 0.8314 (p0) outliers start: 34 outliers final: 26 residues processed: 208 average time/residue: 0.0525 time to fit residues: 16.5500 Evaluate side-chains 199 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 81 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 29 optimal weight: 0.0010 chunk 70 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 90 optimal weight: 9.9990 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.111459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098129 restraints weight = 10922.861| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.72 r_work: 0.3385 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.054 7040 Z= 0.387 Angle : 0.780 8.749 9470 Z= 0.414 Chirality : 0.055 0.140 1180 Planarity : 0.003 0.018 1180 Dihedral : 7.333 43.721 1010 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer: Outliers : 10.44 % Allowed : 16.32 % Favored : 73.24 % 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 are not related in a simple way. whole: -4.57 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.13), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.004 PHE G 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00879 / 0.39 ( 7040) covalent geometry : angle 0.78005 / 0.41 ( 9470) hydrogen bonds : bond 0.04506 / 2.70 ( 28) hydrogen bonds : angle 4.91464 / 3.32 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 168 time to evaluate : 0.181 Fit side-chains REVERT: A 42 SER cc_start: 0.9158 (p) cc_final: 0.8942 (p) REVERT: B 32 LYS cc_start: 0.9086 (ttpt) cc_final: 0.8836 (mtpp) REVERT: D 2 ASP cc_start: 0.8923 (p0) cc_final: 0.8545 (p0) REVERT: E 26 VAL cc_start: 0.9399 (m) cc_final: 0.9108 (t) REVERT: E 32 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8742 (mtpt) REVERT: G 32 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8719 (mtpp) REVERT: H 2 ASP cc_start: 0.8849 (p0) cc_final: 0.8509 (p0) REVERT: J 2 ASP cc_start: 0.8909 (p0) cc_final: 0.8674 (p0) outliers start: 71 outliers final: 67 residues processed: 215 average time/residue: 0.0507 time to fit residues: 16.5817 Evaluate side-chains 228 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 161 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 71 optimal weight: 9.9990 chunk 48 optimal weight: 0.0470 chunk 81 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.118779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104747 restraints weight = 10799.896| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.81 r_work: 0.3503 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7040 Z= 0.139 Angle : 0.612 7.258 9470 Z= 0.319 Chirality : 0.048 0.141 1180 Planarity : 0.002 0.013 1180 Dihedral : 6.425 43.908 1010 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 9.26 % Allowed : 18.68 % Favored : 72.06 % 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 are not related in a simple way. whole: -4.18 (0.19), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE B 94 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 7040) covalent geometry : angle 0.61202 / 0.32 ( 9470) hydrogen bonds : bond 0.03115 / 1.92 ( 28) hydrogen bonds : angle 4.50933 / 3.00 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 188 time to evaluate : 0.255 Fit side-chains REVERT: B 13 GLU cc_start: 0.8137 (tp30) cc_final: 0.7368 (tp30) REVERT: D 2 ASP cc_start: 0.8895 (p0) cc_final: 0.8492 (p0) REVERT: D 8 LEU cc_start: 0.9189 (mm) cc_final: 0.8830 (mm) REVERT: E 32 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8585 (mtpt) REVERT: G 32 LYS cc_start: 0.9087 (ttpt) cc_final: 0.8698 (mtpt) REVERT: H 2 ASP cc_start: 0.8794 (p0) cc_final: 0.8413 (p0) REVERT: J 2 ASP cc_start: 0.9002 (p0) cc_final: 0.8778 (p0) outliers start: 63 outliers final: 54 residues processed: 221 average time/residue: 0.0488 time to fit residues: 16.7619 Evaluate side-chains 237 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 99 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 9 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.109764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.095795 restraints weight = 11201.304| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 2.77 r_work: 0.3359 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.064 7040 Z= 0.479 Angle : 0.853 8.670 9470 Z= 0.452 Chirality : 0.059 0.183 1180 Planarity : 0.003 0.014 1180 Dihedral : 7.525 44.612 1010 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 12.21 % Allowed : 16.76 % Favored : 71.03 % 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 are not related in a simple way. whole: -4.44 (0.18), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.027 0.004 PHE J 94 HIS 0.008 0.004 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.01088 / 0.48 ( 7040) covalent geometry : angle 0.85309 / 0.45 ( 9470) hydrogen bonds : bond 0.04463 / 2.66 ( 28) hydrogen bonds : angle 4.92118 / 3.28 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 169 time to evaluate : 0.256 Fit side-chains REVERT: B 32 LYS cc_start: 0.9136 (ttpt) cc_final: 0.8898 (mtpp) REVERT: D 2 ASP cc_start: 0.8894 (p0) cc_final: 0.8498 (p0) REVERT: E 32 LYS cc_start: 0.9107 (ttpt) cc_final: 0.8794 (mtpt) REVERT: F 13 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7575 (tm-30) REVERT: G 32 LYS cc_start: 0.9109 (ttpt) cc_final: 0.8729 (mtpt) REVERT: H 2 ASP cc_start: 0.8714 (p0) cc_final: 0.8295 (p0) REVERT: I 42 SER cc_start: 0.9627 (p) cc_final: 0.9404 (p) REVERT: J 2 ASP cc_start: 0.8886 (p0) cc_final: 0.8677 (p0) outliers start: 83 outliers final: 78 residues processed: 229 average time/residue: 0.0506 time to fit residues: 17.8223 Evaluate side-chains 242 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 164 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 55 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 70 VAL Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.119273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.105310 restraints weight = 10798.457| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.79 r_work: 0.3505 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7040 Z= 0.125 Angle : 0.615 7.734 9470 Z= 0.317 Chirality : 0.048 0.137 1180 Planarity : 0.002 0.016 1180 Dihedral : 6.444 43.879 1010 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 10.29 % Allowed : 18.82 % Favored : 70.88 % 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 are not related in a simple way. whole: -4.11 (0.19), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE C 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 7040) covalent geometry : angle 0.61547 / 0.32 ( 9470) hydrogen bonds : bond 0.02847 / 1.76 ( 28) hydrogen bonds : angle 4.44245 / 2.91 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 185 time to evaluate : 0.274 Fit side-chains REVERT: B 13 GLU cc_start: 0.8019 (tp30) cc_final: 0.7788 (tp30) REVERT: D 2 ASP cc_start: 0.8807 (p0) cc_final: 0.8384 (p0) REVERT: D 8 LEU cc_start: 0.9177 (mm) cc_final: 0.8817 (mm) REVERT: E 32 LYS cc_start: 0.8943 (ttpt) cc_final: 0.8619 (mtpt) REVERT: G 28 GLU cc_start: 0.8322 (tt0) cc_final: 0.8017 (mt-10) REVERT: G 32 LYS cc_start: 0.9061 (ttpt) cc_final: 0.8696 (mtpt) outliers start: 70 outliers final: 65 residues processed: 225 average time/residue: 0.0515 time to fit residues: 17.8404 Evaluate side-chains 244 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 179 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.111487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.097488 restraints weight = 11026.776| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.80 r_work: 0.3392 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 7040 Z= 0.351 Angle : 0.763 8.506 9470 Z= 0.400 Chirality : 0.054 0.138 1180 Planarity : 0.003 0.015 1180 Dihedral : 7.172 43.959 1010 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.89 % Favored : 86.11 % Rotamer: Outliers : 11.18 % Allowed : 18.53 % Favored : 70.29 % 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 are not related in a simple way. whole: -4.22 (0.19), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.14), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.022 0.004 PHE G 94 HIS 0.007 0.003 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00797 / 0.35 ( 7040) covalent geometry : angle 0.76287 / 0.40 ( 9470) hydrogen bonds : bond 0.03894 / 2.29 ( 28) hydrogen bonds : angle 4.68516 / 3.11 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 170 time to evaluate : 0.263 Fit side-chains REVERT: B 32 LYS cc_start: 0.9076 (ttpt) cc_final: 0.8811 (mtpp) REVERT: B 83 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: C 13 GLU cc_start: 0.8456 (tp30) cc_final: 0.8213 (tp30) REVERT: D 2 ASP cc_start: 0.8800 (p0) cc_final: 0.8366 (p0) REVERT: E 32 LYS cc_start: 0.9105 (ttpt) cc_final: 0.8768 (mtpt) REVERT: G 32 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8764 (mtpp) outliers start: 76 outliers final: 72 residues processed: 221 average time/residue: 0.0485 time to fit residues: 16.4857 Evaluate side-chains 241 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 168 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 MET Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.120217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.106229 restraints weight = 10802.978| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.80 r_work: 0.3532 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7040 Z= 0.117 Angle : 0.617 8.512 9470 Z= 0.318 Chirality : 0.048 0.139 1180 Planarity : 0.002 0.014 1180 Dihedral : 6.307 43.351 1010 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 10.00 % Allowed : 19.56 % Favored : 70.44 % 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 are not related in a simple way. whole: -3.94 (0.20), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 7040) covalent geometry : angle 0.61737 / 0.32 ( 9470) hydrogen bonds : bond 0.02657 / 1.62 ( 28) hydrogen bonds : angle 4.35031 / 2.84 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 191 time to evaluate : 0.257 Fit side-chains REVERT: D 2 ASP cc_start: 0.8714 (p0) cc_final: 0.8283 (p0) REVERT: D 8 LEU cc_start: 0.9169 (mm) cc_final: 0.8803 (mm) REVERT: E 32 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8603 (mtpt) REVERT: G 32 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8683 (mtpt) REVERT: I 32 LYS cc_start: 0.8979 (ttmt) cc_final: 0.8471 (ttmt) outliers start: 68 outliers final: 63 residues processed: 229 average time/residue: 0.0498 time to fit residues: 17.4439 Evaluate side-chains 248 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 185 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 9.9990 chunk 97 optimal weight: 0.0980 chunk 82 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 GLN J 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.111405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.097314 restraints weight = 11079.522| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 2.81 r_work: 0.3394 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 7040 Z= 0.356 Angle : 0.787 8.331 9470 Z= 0.409 Chirality : 0.054 0.140 1180 Planarity : 0.003 0.016 1180 Dihedral : 7.154 44.151 1010 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 11.03 % Allowed : 19.26 % Favored : 69.71 % 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 are not related in a simple way. whole: -4.10 (0.19), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.004 PHE G 94 HIS 0.006 0.003 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.36 ( 7040) covalent geometry : angle 0.78671 / 0.41 ( 9470) hydrogen bonds : bond 0.03889 / 2.29 ( 28) hydrogen bonds : angle 4.69563 / 3.12 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 169 time to evaluate : 0.272 Fit side-chains REVERT: B 32 LYS cc_start: 0.9057 (ttpt) cc_final: 0.8810 (mtpp) REVERT: B 83 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: C 13 GLU cc_start: 0.8286 (tp30) cc_final: 0.8040 (tp30) REVERT: D 2 ASP cc_start: 0.8620 (p0) cc_final: 0.8197 (p0) REVERT: E 32 LYS cc_start: 0.8997 (ttpt) cc_final: 0.8649 (mtpt) REVERT: G 32 LYS cc_start: 0.9027 (ttpt) cc_final: 0.8666 (mtpp) REVERT: J 26 VAL cc_start: 0.9253 (m) cc_final: 0.9040 (t) outliers start: 75 outliers final: 68 residues processed: 219 average time/residue: 0.0540 time to fit residues: 18.0802 Evaluate side-chains 236 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 167 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 70 VAL Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.8980 chunk 82 optimal weight: 0.0670 chunk 27 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.120238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.106188 restraints weight = 10767.691| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.80 r_work: 0.3528 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7040 Z= 0.123 Angle : 0.656 8.502 9470 Z= 0.336 Chirality : 0.048 0.154 1180 Planarity : 0.002 0.020 1180 Dihedral : 6.368 43.943 1010 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 9.56 % Allowed : 20.00 % Favored : 70.44 % 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 are not related in a simple way. whole: -3.86 (0.20), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.15), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 7040) covalent geometry : angle 0.65627 / 0.34 ( 9470) hydrogen bonds : bond 0.02673 / 1.61 ( 28) hydrogen bonds : angle 4.35218 / 2.85 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 184 time to evaluate : 0.272 Fit side-chains REVERT: D 2 ASP cc_start: 0.8622 (p0) cc_final: 0.8216 (p0) REVERT: D 8 LEU cc_start: 0.9184 (mm) cc_final: 0.8823 (mm) REVERT: E 32 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8575 (mtpt) REVERT: G 28 GLU cc_start: 0.8343 (tt0) cc_final: 0.8065 (mt-10) REVERT: G 32 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8691 (mtpt) outliers start: 65 outliers final: 64 residues processed: 226 average time/residue: 0.0509 time to fit residues: 17.7190 Evaluate side-chains 244 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 42 SER Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain E residue 22 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 54 THR Chi-restraints excluded: chain G residue 55 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 5 MET Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 71 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 28 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.120811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106830 restraints weight = 10452.703| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.70 r_work: 0.3546 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7040 Z= 0.135 Angle : 0.625 8.430 9470 Z= 0.322 Chirality : 0.048 0.134 1180 Planarity : 0.002 0.017 1180 Dihedral : 6.242 43.865 1010 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 9.85 % Allowed : 20.44 % Favored : 69.71 % 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 are not related in a simple way. whole: -3.76 (0.20), residues: 950 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.86 (0.16), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE B 94 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 7040) covalent geometry : angle 0.62546 / 0.32 ( 9470) hydrogen bonds : bond 0.02690 / 1.59 ( 28) hydrogen bonds : angle 4.26321 / 2.80 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1486.91 seconds wall clock time: 26 minutes 21.64 seconds (1581.64 seconds total)