Starting phenix.real_space_refine on Fri Aug 22 14:36:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ufr_20759/08_2025/6ufr_20759.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ufr_20759/08_2025/6ufr_20759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ufr_20759/08_2025/6ufr_20759.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ufr_20759/08_2025/6ufr_20759.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ufr_20759/08_2025/6ufr_20759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ufr_20759/08_2025/6ufr_20759.map" } resolution = 2.5 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2720 2.51 5 N 760 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4420 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "J" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Restraints were copied for chains: C, E, G, I, F, J, D, H, B Time building chain proxies: 0.79, per 1000 atoms: 0.18 Number of scatterers: 4420 At special positions: 0 Unit cell: (103.074, 96.37, 41.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 940 8.00 N 760 7.00 C 2720 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: 0.35 Conformation dependent library (CDL) restraints added in 471.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 68.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 37 through 57 removed outlier: 9.090A pdb=" N VAL E 37 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 9.953A pdb=" N VAL D 40 " --> pdb=" O VAL E 37 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N TYR E 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 10.066A pdb=" N SER D 42 " --> pdb=" O TYR E 39 " (cutoff:3.500A) removed outlier: 8.994A pdb=" N GLY E 41 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N THR D 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LYS E 43 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N LYS D 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS E 45 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL D 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY E 47 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N HIS D 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL E 49 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N VAL D 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N GLY E 51 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 10.333A pdb=" N THR D 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N ALA E 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 10.023A pdb=" N ALA D 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N VAL E 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU A 38 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 39 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL A 40 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY D 41 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER A 42 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LYS D 43 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N THR A 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LYS D 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA D 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR A 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL D 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA A 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU D 57 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU H 38 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR A 39 " --> pdb=" O LEU H 38 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N VAL H 40 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N GLY A 41 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N SER H 42 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS A 43 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N THR H 44 " --> pdb=" O LYS A 43 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYS A 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL H 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ALA A 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR H 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 55 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA H 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU A 57 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.135A pdb=" N LEU I 38 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 10.139A pdb=" N GLY H 41 " --> pdb=" O LEU I 38 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N VAL I 40 " --> pdb=" O GLY H 41 " (cutoff:3.500A) removed outlier: 10.437A pdb=" N LYS H 43 " --> pdb=" O VAL I 40 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N SER I 42 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N LYS H 45 " --> pdb=" O SER I 42 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR I 44 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY H 47 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS I 46 " --> pdb=" O GLY H 47 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL H 49 " --> pdb=" O LYS I 46 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL I 48 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N GLY H 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N HIS I 50 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ALA H 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL I 52 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N VAL H 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N THR I 54 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 10.341A pdb=" N GLU H 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N ALA I 56 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 61 through 66 removed outlier: 6.751A pdb=" N GLU A 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N THR D 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL A 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL D 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASN A 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU I 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N THR H 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL I 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL H 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ASN I 65 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 70 through 72 removed outlier: 6.395A pdb=" N VAL A 70 " --> pdb=" O VAL H 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 76 through 83 removed outlier: 6.616A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N THR D 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N GLU D 83 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA I 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN H 79 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA I 78 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N THR H 81 " --> pdb=" O ALA I 78 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS I 80 " --> pdb=" O THR H 81 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLU H 83 " --> pdb=" O LYS I 80 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL I 82 " --> pdb=" O GLU H 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 88 through 97 removed outlier: 6.335A pdb=" N ILE E 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ALA D 91 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA E 90 " --> pdb=" O ALA D 91 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N GLY D 93 " --> pdb=" O ALA E 90 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N THR E 92 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N VAL D 95 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N PHE E 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 10.295A pdb=" N LYS D 97 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N LYS E 96 " --> pdb=" O LYS D 97 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE D 94 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 95 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LYS D 96 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LYS A 97 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ILE A 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ALA H 91 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLY H 93 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR A 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL H 95 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N PHE A 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 10.275A pdb=" N LYS H 97 " --> pdb=" O PHE A 94 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N LYS A 96 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ILE I 88 " --> pdb=" O ALA H 89 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N ALA H 91 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 9.023A pdb=" N ALA I 90 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLY H 93 " --> pdb=" O ALA I 90 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N THR I 92 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL H 95 " --> pdb=" O THR I 92 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE I 94 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS H 97 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS I 96 " --> pdb=" O LYS H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 37 through 57 removed outlier: 9.128A pdb=" N LEU C 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) removed outlier: 10.126A pdb=" N GLY F 41 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N VAL C 40 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 10.409A pdb=" N LYS F 43 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 9.175A pdb=" N SER C 42 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N LYS F 45 " --> pdb=" O SER C 42 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N THR C 44 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY F 47 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS C 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N VAL F 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL C 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY F 51 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 8.575A pdb=" N HIS C 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ALA F 53 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.099A pdb=" N VAL C 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL F 55 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N THR C 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 10.382A pdb=" N GLU F 57 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA C 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N VAL C 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 10.025A pdb=" N VAL B 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N TYR C 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 10.146A pdb=" N SER B 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N GLY C 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 10.185A pdb=" N THR B 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N LYS C 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 9.860A pdb=" N LYS B 46 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 45 " --> pdb=" O LYS B 46 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL B 48 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY C 47 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N HIS B 50 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 49 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N VAL B 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N GLY C 51 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 10.363A pdb=" N THR B 54 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N ALA C 53 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 10.042A pdb=" N ALA B 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 9.040A pdb=" N VAL C 55 " --> pdb=" O ALA B 56 " (cutoff:3.500A) removed outlier: 9.101A pdb=" N LEU G 38 " --> pdb=" O TYR B 39 " (cutoff:3.500A) removed outlier: 10.088A pdb=" N GLY B 41 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 9.078A pdb=" N VAL G 40 " --> pdb=" O GLY B 41 " (cutoff:3.500A) removed outlier: 10.357A pdb=" N LYS B 43 " --> pdb=" O VAL G 40 " (cutoff:3.500A) removed outlier: 9.116A pdb=" N SER G 42 " --> pdb=" O LYS B 43 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N LYS B 45 " --> pdb=" O SER G 42 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N THR G 44 " --> pdb=" O LYS B 45 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N GLY B 47 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS G 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 49 " --> pdb=" O LYS G 46 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL G 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N GLY B 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N HIS G 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N ALA B 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N VAL G 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N VAL B 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 9.177A pdb=" N THR G 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.355A pdb=" N GLU B 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N ALA G 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU J 38 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N TYR G 39 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL J 40 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N GLY G 41 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER J 42 " --> pdb=" O GLY G 41 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LYS G 43 " --> pdb=" O SER J 42 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR J 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 45 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL J 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA G 53 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR J 54 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL G 55 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA J 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLU G 57 " --> pdb=" O ALA J 56 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 66 removed outlier: 6.717A pdb=" N GLU C 61 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N THR F 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL C 63 " --> pdb=" O THR F 64 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL F 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN C 65 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLU G 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N THR B 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL G 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL B 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN G 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 70 through 72 removed outlier: 6.433A pdb=" N VAL C 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 76 through 83 removed outlier: 6.620A pdb=" N ALA C 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLN F 79 " --> pdb=" O ALA C 76 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ALA C 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N THR F 81 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LYS C 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N GLU F 83 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA G 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLN B 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA G 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N THR B 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS G 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N GLU B 83 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL G 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 88 through 97 removed outlier: 6.755A pdb=" N PHE F 94 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL C 95 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LYS F 96 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS C 97 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE C 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA B 91 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C 90 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N GLY B 93 " --> pdb=" O ALA C 90 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N THR C 92 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL B 95 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N PHE C 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 10.269A pdb=" N LYS B 97 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 9.299A pdb=" N LYS C 96 " --> pdb=" O LYS B 97 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE B 94 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL G 95 " --> pdb=" O PHE B 94 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LYS B 96 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS G 97 " --> pdb=" O LYS B 96 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA G 89 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA J 90 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA G 91 " --> pdb=" O ALA J 90 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N THR J 92 " --> pdb=" O ALA G 91 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLY G 93 " --> pdb=" O THR J 92 " (cutoff:3.500A) 95 hydrogen bonds defined for protein. 285 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: 0.70 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.28: 740 1.28 - 1.35: 670 1.35 - 1.41: 170 1.41 - 1.48: 769 1.48 - 1.54: 2001 Bond restraints: 4350 Sorted by residual: bond pdb=" N GLU J 83 " pdb=" CA GLU J 83 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.20e-02 6.94e+03 5.52e+00 bond pdb=" N GLU F 83 " pdb=" CA GLU F 83 " ideal model delta sigma weight residual 1.460 1.488 -0.028 1.20e-02 6.94e+03 5.30e+00 bond pdb=" N GLU G 83 " pdb=" CA GLU G 83 " ideal model delta sigma weight residual 1.460 1.487 -0.028 1.20e-02 6.94e+03 5.28e+00 bond pdb=" N GLU A 83 " pdb=" CA GLU A 83 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.19e+00 bond pdb=" N GLU H 83 " pdb=" CA GLU H 83 " ideal model delta sigma weight residual 1.460 1.487 -0.027 1.20e-02 6.94e+03 5.18e+00 ... (remaining 4345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 4955 1.19 - 2.38: 701 2.38 - 3.58: 177 3.58 - 4.77: 27 4.77 - 5.96: 10 Bond angle restraints: 5870 Sorted by residual: angle pdb=" C THR H 59 " pdb=" N LYS H 60 " pdb=" CA LYS H 60 " ideal model delta sigma weight residual 122.42 118.11 4.31 1.55e+00 4.16e-01 7.74e+00 angle pdb=" C THR F 59 " pdb=" N LYS F 60 " pdb=" CA LYS F 60 " ideal model delta sigma weight residual 122.42 118.12 4.30 1.55e+00 4.16e-01 7.69e+00 angle pdb=" C THR J 59 " pdb=" N LYS J 60 " pdb=" CA LYS J 60 " ideal model delta sigma weight residual 122.42 118.13 4.29 1.55e+00 4.16e-01 7.64e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.42 118.14 4.28 1.55e+00 4.16e-01 7.62e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.42 118.15 4.27 1.55e+00 4.16e-01 7.59e+00 ... (remaining 5865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 2330 14.90 - 29.80: 150 29.80 - 44.70: 20 44.70 - 59.60: 30 59.60 - 74.50: 10 Dihedral angle restraints: 2540 sinusoidal: 850 harmonic: 1690 Sorted by residual: dihedral pdb=" CA GLY E 73 " pdb=" C GLY E 73 " pdb=" N VAL E 74 " pdb=" CA VAL E 74 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY C 73 " pdb=" C GLY C 73 " pdb=" N VAL C 74 " pdb=" CA VAL C 74 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA GLY A 73 " pdb=" C GLY A 73 " pdb=" N VAL A 74 " pdb=" CA VAL A 74 " ideal model delta harmonic sigma weight residual 180.00 159.71 20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 2537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 289 0.040 - 0.079: 232 0.079 - 0.118: 199 0.118 - 0.157: 35 0.157 - 0.197: 15 Chirality restraints: 770 Sorted by residual: chirality pdb=" CB THR E 44 " pdb=" CA THR E 44 " pdb=" OG1 THR E 44 " pdb=" CG2 THR E 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.67e-01 chirality pdb=" CB THR B 44 " pdb=" CA THR B 44 " pdb=" OG1 THR B 44 " pdb=" CG2 THR B 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CB THR H 44 " pdb=" CA THR H 44 " pdb=" OG1 THR H 44 " pdb=" CG2 THR H 44 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.39e-01 ... (remaining 767 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 75 " -0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C THR C 75 " 0.064 2.00e-02 2.50e+03 pdb=" O THR C 75 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA C 76 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 75 " 0.019 2.00e-02 2.50e+03 3.72e-02 1.39e+01 pdb=" C THR D 75 " -0.064 2.00e-02 2.50e+03 pdb=" O THR D 75 " 0.024 2.00e-02 2.50e+03 pdb=" N ALA D 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 75 " -0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C THR B 75 " 0.064 2.00e-02 2.50e+03 pdb=" O THR B 75 " -0.024 2.00e-02 2.50e+03 pdb=" N ALA B 76 " -0.022 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 351 2.75 - 3.29: 3533 3.29 - 3.82: 7636 3.82 - 4.36: 8344 4.36 - 4.90: 16105 Nonbonded interactions: 35969 Sorted by model distance: nonbonded pdb=" O GLY D 67 " pdb=" O HOH D 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY J 67 " pdb=" O HOH J 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY C 67 " pdb=" O HOH C 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY H 67 " pdb=" O HOH H 201 " model vdw 2.209 3.040 nonbonded pdb=" O GLY I 67 " pdb=" O HOH I 201 " model vdw 2.209 3.040 ... (remaining 35964 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'F' selection = chain 'J' selection = chain 'D' selection = chain 'H' selection = chain 'B' } 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.720 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 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:7.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 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 : 0.012 0.061 4350 Z= 0.493 Angle : 0.960 5.959 5870 Z= 0.568 Chirality : 0.071 0.197 770 Planarity : 0.009 0.037 720 Dihedral : 13.714 74.498 1480 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.99 (0.27), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.21), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.003 TYR D 39 PHE 0.018 0.005 PHE G 94 HIS 0.003 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.01228 ( 4350) covalent geometry : angle 0.96006 ( 5870) hydrogen bonds : bond 0.09747 ( 95) hydrogen bonds : angle 8.56883 ( 285) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.175 Fit side-chains REVERT: A 43 LYS cc_start: 0.8214 (mttt) cc_final: 0.7968 (mptt) REVERT: A 57 GLU cc_start: 0.8060 (tt0) cc_final: 0.7850 (tm-30) REVERT: A 83 GLU cc_start: 0.7374 (mt-10) cc_final: 0.7070 (mp0) REVERT: C 43 LYS cc_start: 0.8461 (mttt) cc_final: 0.8154 (mptt) REVERT: C 57 GLU cc_start: 0.8094 (tt0) cc_final: 0.7891 (tm-30) REVERT: C 81 THR cc_start: 0.9027 (m) cc_final: 0.8503 (m) REVERT: C 83 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6879 (mp0) REVERT: E 43 LYS cc_start: 0.8360 (mttt) cc_final: 0.8145 (mptt) REVERT: E 57 GLU cc_start: 0.7880 (tt0) cc_final: 0.7613 (tm-30) REVERT: G 43 LYS cc_start: 0.8243 (mttt) cc_final: 0.8006 (mptt) REVERT: G 46 LYS cc_start: 0.8557 (tttt) cc_final: 0.7979 (tmtm) REVERT: G 83 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6892 (mp0) REVERT: I 46 LYS cc_start: 0.8667 (tttt) cc_final: 0.8032 (tmtm) REVERT: F 43 LYS cc_start: 0.8309 (mttt) cc_final: 0.8090 (mptt) REVERT: F 57 GLU cc_start: 0.7929 (tt0) cc_final: 0.7633 (tm-30) REVERT: J 46 LYS cc_start: 0.8686 (tttt) cc_final: 0.8038 (tmtm) REVERT: D 43 LYS cc_start: 0.8330 (mttt) cc_final: 0.8046 (mptt) REVERT: D 57 GLU cc_start: 0.8098 (tt0) cc_final: 0.7898 (tm-30) REVERT: D 81 THR cc_start: 0.9061 (m) cc_final: 0.8495 (m) REVERT: D 83 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6922 (mp0) REVERT: H 43 LYS cc_start: 0.8130 (mttt) cc_final: 0.7882 (mptt) REVERT: H 46 LYS cc_start: 0.8564 (tttt) cc_final: 0.8072 (tmtm) REVERT: H 83 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6717 (mp0) REVERT: B 43 LYS cc_start: 0.8388 (mttt) cc_final: 0.8147 (mptt) REVERT: B 46 LYS cc_start: 0.8597 (tttt) cc_final: 0.8348 (tmtp) REVERT: B 57 GLU cc_start: 0.7998 (tt0) cc_final: 0.7795 (tm-30) REVERT: B 83 GLU cc_start: 0.7364 (mt-10) cc_final: 0.6901 (mp0) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.4923 time to fit residues: 70.9136 Evaluate side-chains 128 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.139223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.123077 restraints weight = 3920.042| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.60 r_work: 0.3614 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4350 Z= 0.126 Angle : 0.543 6.171 5870 Z= 0.303 Chirality : 0.055 0.131 770 Planarity : 0.002 0.008 720 Dihedral : 5.695 17.481 630 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.55 % Allowed : 15.45 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 39 PHE 0.016 0.003 PHE J 94 HIS 0.001 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 4350) covalent geometry : angle 0.54255 ( 5870) hydrogen bonds : bond 0.02027 ( 95) hydrogen bonds : angle 6.32412 ( 285) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.175 Fit side-chains REVERT: A 43 LYS cc_start: 0.8582 (mttt) cc_final: 0.8015 (mptt) REVERT: A 57 GLU cc_start: 0.8625 (tt0) cc_final: 0.8210 (tm-30) REVERT: A 83 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7265 (mp0) REVERT: C 43 LYS cc_start: 0.8634 (mttt) cc_final: 0.8014 (mptt) REVERT: C 57 GLU cc_start: 0.8664 (tt0) cc_final: 0.8313 (tm-30) REVERT: C 81 THR cc_start: 0.9065 (m) cc_final: 0.8810 (m) REVERT: C 83 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7204 (mp0) REVERT: E 57 GLU cc_start: 0.8358 (tt0) cc_final: 0.7960 (tm-30) REVERT: G 43 LYS cc_start: 0.8601 (mttt) cc_final: 0.8000 (mptt) REVERT: G 46 LYS cc_start: 0.8944 (tttt) cc_final: 0.8345 (tmtm) REVERT: G 83 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7163 (mp0) REVERT: I 43 LYS cc_start: 0.8481 (mptt) cc_final: 0.8180 (mptt) REVERT: I 46 LYS cc_start: 0.8934 (tttt) cc_final: 0.8296 (tmtm) REVERT: F 57 GLU cc_start: 0.8388 (tt0) cc_final: 0.7972 (tm-30) REVERT: J 43 LYS cc_start: 0.8417 (mptt) cc_final: 0.8175 (mptt) REVERT: J 46 LYS cc_start: 0.8879 (tttt) cc_final: 0.8256 (tmtm) REVERT: J 57 GLU cc_start: 0.8603 (tt0) cc_final: 0.8194 (tm-30) REVERT: D 43 LYS cc_start: 0.8607 (mttt) cc_final: 0.7976 (mptt) REVERT: D 57 GLU cc_start: 0.8662 (tt0) cc_final: 0.8299 (tm-30) REVERT: D 81 THR cc_start: 0.9091 (m) cc_final: 0.8746 (m) REVERT: D 83 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7215 (mp0) REVERT: H 43 LYS cc_start: 0.8617 (mttt) cc_final: 0.8055 (mptt) REVERT: H 46 LYS cc_start: 0.8820 (tttt) cc_final: 0.8291 (tmtm) REVERT: H 83 GLU cc_start: 0.8011 (mt-10) cc_final: 0.7160 (mp0) REVERT: B 43 LYS cc_start: 0.8637 (mttt) cc_final: 0.8050 (mptt) REVERT: B 57 GLU cc_start: 0.8643 (tt0) cc_final: 0.8188 (tm-30) REVERT: B 83 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7323 (mp0) outliers start: 20 outliers final: 8 residues processed: 129 average time/residue: 0.4884 time to fit residues: 65.2578 Evaluate side-chains 125 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 117 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 58 optimal weight: 20.0000 chunk 47 optimal weight: 50.0000 chunk 11 optimal weight: 50.0000 chunk 6 optimal weight: 30.0000 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 25 optimal weight: 40.0000 chunk 33 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 40.0000 chunk 26 optimal weight: 30.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.133251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.117122 restraints weight = 3981.820| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.62 r_work: 0.3544 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4350 Z= 0.181 Angle : 0.598 6.322 5870 Z= 0.334 Chirality : 0.056 0.144 770 Planarity : 0.002 0.009 720 Dihedral : 6.036 18.873 630 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 15.23 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.002 TYR E 39 PHE 0.016 0.004 PHE G 94 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4350) covalent geometry : angle 0.59770 ( 5870) hydrogen bonds : bond 0.02440 ( 95) hydrogen bonds : angle 5.97468 ( 285) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 0.186 Fit side-chains REVERT: A 43 LYS cc_start: 0.8744 (mttt) cc_final: 0.8099 (mptt) REVERT: A 46 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8244 (tmtp) REVERT: A 57 GLU cc_start: 0.8674 (tt0) cc_final: 0.8185 (tm-30) REVERT: A 83 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7658 (mp0) REVERT: C 43 LYS cc_start: 0.8748 (mttt) cc_final: 0.8054 (mptt) REVERT: C 57 GLU cc_start: 0.8737 (tt0) cc_final: 0.8331 (tm-30) REVERT: E 43 LYS cc_start: 0.8611 (mttt) cc_final: 0.7979 (mptt) REVERT: E 57 GLU cc_start: 0.8423 (tt0) cc_final: 0.8007 (tm-30) REVERT: G 43 LYS cc_start: 0.8596 (mttt) cc_final: 0.7959 (mptt) REVERT: G 46 LYS cc_start: 0.8880 (tttt) cc_final: 0.8265 (tmtm) REVERT: G 83 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7295 (mp0) REVERT: I 57 GLU cc_start: 0.8635 (tt0) cc_final: 0.8236 (tm-30) REVERT: I 83 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7501 (mp0) REVERT: F 43 LYS cc_start: 0.8609 (mttt) cc_final: 0.7966 (mptt) REVERT: F 57 GLU cc_start: 0.8430 (tt0) cc_final: 0.8008 (tm-30) REVERT: J 57 GLU cc_start: 0.8644 (tt0) cc_final: 0.8243 (tm-30) REVERT: J 83 GLU cc_start: 0.8463 (mt-10) cc_final: 0.7596 (mp0) REVERT: D 43 LYS cc_start: 0.8733 (mttt) cc_final: 0.8046 (mptt) REVERT: D 57 GLU cc_start: 0.8728 (tt0) cc_final: 0.8314 (tm-30) REVERT: H 43 LYS cc_start: 0.8615 (mttt) cc_final: 0.7988 (mptt) REVERT: H 46 LYS cc_start: 0.8821 (tttt) cc_final: 0.8229 (tmtm) REVERT: H 83 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7296 (mp0) REVERT: B 43 LYS cc_start: 0.8757 (mttt) cc_final: 0.8120 (mptt) REVERT: B 57 GLU cc_start: 0.8689 (tt0) cc_final: 0.8181 (tm-30) REVERT: B 83 GLU cc_start: 0.8438 (mt-10) cc_final: 0.7662 (mp0) outliers start: 24 outliers final: 16 residues processed: 123 average time/residue: 0.5576 time to fit residues: 70.9289 Evaluate side-chains 128 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 20.0000 chunk 38 optimal weight: 0.0060 chunk 53 optimal weight: 40.0000 chunk 24 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 3 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 overall best weight: 14.0010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114250 restraints weight = 3948.140| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.59 r_work: 0.3515 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3415 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 4350 Z= 0.243 Angle : 0.683 7.076 5870 Z= 0.380 Chirality : 0.058 0.156 770 Planarity : 0.003 0.012 720 Dihedral : 6.350 19.824 630 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.45 % Allowed : 13.64 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR E 39 PHE 0.017 0.005 PHE G 94 HIS 0.003 0.001 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 4350) covalent geometry : angle 0.68287 ( 5870) hydrogen bonds : bond 0.02777 ( 95) hydrogen bonds : angle 5.94039 ( 285) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 0.181 Fit side-chains REVERT: A 43 LYS cc_start: 0.8726 (mttt) cc_final: 0.8045 (mptt) REVERT: A 46 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8191 (tmtp) REVERT: A 57 GLU cc_start: 0.8681 (tt0) cc_final: 0.8153 (tm-30) REVERT: C 43 LYS cc_start: 0.8743 (mttt) cc_final: 0.8036 (mptt) REVERT: C 46 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8201 (tmtp) REVERT: C 57 GLU cc_start: 0.8740 (tt0) cc_final: 0.8315 (tm-30) REVERT: E 43 LYS cc_start: 0.8690 (mttt) cc_final: 0.7991 (mptt) REVERT: E 57 GLU cc_start: 0.8423 (tt0) cc_final: 0.8000 (tm-30) REVERT: G 43 LYS cc_start: 0.8619 (mttt) cc_final: 0.7959 (mptt) REVERT: G 46 LYS cc_start: 0.8863 (tttt) cc_final: 0.8263 (tmtm) REVERT: G 83 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7273 (mp0) REVERT: I 46 LYS cc_start: 0.8915 (tmtp) cc_final: 0.8277 (tmtm) REVERT: I 57 GLU cc_start: 0.8598 (tt0) cc_final: 0.8257 (tm-30) REVERT: F 43 LYS cc_start: 0.8695 (mttt) cc_final: 0.7985 (mptt) REVERT: F 57 GLU cc_start: 0.8431 (tt0) cc_final: 0.7976 (tm-30) REVERT: J 46 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8153 (tmtm) REVERT: J 57 GLU cc_start: 0.8659 (tt0) cc_final: 0.8263 (tm-30) REVERT: D 43 LYS cc_start: 0.8741 (mttt) cc_final: 0.8043 (mptt) REVERT: D 57 GLU cc_start: 0.8735 (tt0) cc_final: 0.8306 (tm-30) REVERT: D 83 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7464 (mp0) REVERT: H 43 LYS cc_start: 0.8655 (mttt) cc_final: 0.7969 (mptt) REVERT: H 46 LYS cc_start: 0.8787 (tttt) cc_final: 0.8131 (tmtm) REVERT: B 43 LYS cc_start: 0.8751 (mttt) cc_final: 0.8057 (mptt) REVERT: B 57 GLU cc_start: 0.8705 (tt0) cc_final: 0.8228 (tm-30) outliers start: 24 outliers final: 16 residues processed: 117 average time/residue: 0.5534 time to fit residues: 66.8471 Evaluate side-chains 126 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 40 optimal weight: 7.9990 chunk 18 optimal weight: 30.0000 chunk 39 optimal weight: 30.0000 chunk 13 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 30.0000 chunk 5 optimal weight: 50.0000 chunk 41 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.134101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118237 restraints weight = 3992.035| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.59 r_work: 0.3564 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4350 Z= 0.156 Angle : 0.562 5.997 5870 Z= 0.314 Chirality : 0.055 0.139 770 Planarity : 0.002 0.008 720 Dihedral : 5.786 18.172 630 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 6.14 % Allowed : 13.86 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.34), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.62 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR B 39 PHE 0.015 0.004 PHE G 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 4350) covalent geometry : angle 0.56200 ( 5870) hydrogen bonds : bond 0.02268 ( 95) hydrogen bonds : angle 5.67230 ( 285) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 0.181 Fit side-chains REVERT: A 43 LYS cc_start: 0.8765 (mttt) cc_final: 0.8087 (mptt) REVERT: A 46 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8220 (tmtp) REVERT: A 57 GLU cc_start: 0.8658 (tt0) cc_final: 0.8163 (tm-30) REVERT: C 43 LYS cc_start: 0.8712 (mttt) cc_final: 0.7958 (mptt) REVERT: C 46 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8230 (tmtp) REVERT: C 57 GLU cc_start: 0.8712 (tt0) cc_final: 0.8296 (tm-30) REVERT: E 43 LYS cc_start: 0.8583 (mttt) cc_final: 0.7901 (mptt) REVERT: E 57 GLU cc_start: 0.8405 (tt0) cc_final: 0.8004 (tm-30) REVERT: G 43 LYS cc_start: 0.8666 (mttt) cc_final: 0.8006 (mptt) REVERT: G 46 LYS cc_start: 0.8859 (tttt) cc_final: 0.8291 (tmtm) REVERT: I 46 LYS cc_start: 0.8929 (tmtp) cc_final: 0.8296 (tmtm) REVERT: I 57 GLU cc_start: 0.8623 (tt0) cc_final: 0.8251 (tm-30) REVERT: F 43 LYS cc_start: 0.8624 (mttt) cc_final: 0.7946 (mptt) REVERT: F 57 GLU cc_start: 0.8433 (tt0) cc_final: 0.8021 (tm-30) REVERT: J 46 LYS cc_start: 0.8857 (tmtp) cc_final: 0.8198 (tmtm) REVERT: D 43 LYS cc_start: 0.8697 (mttt) cc_final: 0.7954 (mptt) REVERT: D 57 GLU cc_start: 0.8707 (tt0) cc_final: 0.8292 (tm-30) REVERT: D 83 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7468 (mp0) REVERT: H 43 LYS cc_start: 0.8684 (mttt) cc_final: 0.8022 (mptt) REVERT: H 46 LYS cc_start: 0.8812 (tttt) cc_final: 0.8244 (tmtm) REVERT: B 43 LYS cc_start: 0.8747 (mttt) cc_final: 0.8041 (mptt) REVERT: B 54 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.7975 (m) REVERT: B 57 GLU cc_start: 0.8680 (tt0) cc_final: 0.8214 (tm-30) outliers start: 27 outliers final: 19 residues processed: 123 average time/residue: 0.5023 time to fit residues: 63.9643 Evaluate side-chains 132 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 30.0000 chunk 2 optimal weight: 40.0000 chunk 1 optimal weight: 40.0000 chunk 38 optimal weight: 0.0970 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 54 optimal weight: 20.0000 chunk 17 optimal weight: 40.0000 chunk 59 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 overall best weight: 12.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.131252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.115128 restraints weight = 4050.774| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 1.62 r_work: 0.3527 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4350 Z= 0.218 Angle : 0.645 6.632 5870 Z= 0.360 Chirality : 0.057 0.152 770 Planarity : 0.003 0.011 720 Dihedral : 6.166 19.481 630 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 7.50 % Allowed : 14.09 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.88 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.66 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.013 0.003 TYR A 39 PHE 0.017 0.004 PHE G 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 4350) covalent geometry : angle 0.64533 ( 5870) hydrogen bonds : bond 0.02664 ( 95) hydrogen bonds : angle 5.75551 ( 285) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 109 time to evaluate : 0.129 Fit side-chains REVERT: A 43 LYS cc_start: 0.8810 (mttt) cc_final: 0.8094 (mptt) REVERT: A 46 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8205 (tmtp) REVERT: A 54 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8014 (m) REVERT: A 57 GLU cc_start: 0.8669 (tt0) cc_final: 0.8174 (tm-30) REVERT: C 43 LYS cc_start: 0.8737 (mttt) cc_final: 0.7945 (mptt) REVERT: C 46 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8197 (tmtp) REVERT: C 57 GLU cc_start: 0.8744 (tt0) cc_final: 0.8319 (tm-30) REVERT: E 43 LYS cc_start: 0.8652 (mttt) cc_final: 0.7928 (mptt) REVERT: E 57 GLU cc_start: 0.8429 (tt0) cc_final: 0.8015 (tm-30) REVERT: G 43 LYS cc_start: 0.8634 (mttt) cc_final: 0.7958 (mptt) REVERT: G 46 LYS cc_start: 0.8856 (tttt) cc_final: 0.8254 (tmtm) REVERT: I 46 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8262 (tmtm) REVERT: I 57 GLU cc_start: 0.8641 (tt0) cc_final: 0.8279 (tm-30) REVERT: F 43 LYS cc_start: 0.8662 (mttt) cc_final: 0.7949 (mptt) REVERT: F 57 GLU cc_start: 0.8438 (tt0) cc_final: 0.8010 (tm-30) REVERT: J 46 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8184 (tmtm) REVERT: D 43 LYS cc_start: 0.8719 (mttt) cc_final: 0.7938 (mptt) REVERT: D 46 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8244 (tmtp) REVERT: D 57 GLU cc_start: 0.8736 (tt0) cc_final: 0.8311 (tm-30) REVERT: D 83 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7449 (mp0) REVERT: H 43 LYS cc_start: 0.8626 (mttt) cc_final: 0.7957 (mptt) REVERT: H 46 LYS cc_start: 0.8776 (tttt) cc_final: 0.8175 (tmtm) REVERT: B 43 LYS cc_start: 0.8800 (mttt) cc_final: 0.8069 (mptt) REVERT: B 54 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8002 (m) REVERT: B 57 GLU cc_start: 0.8691 (tt0) cc_final: 0.8187 (tm-30) outliers start: 33 outliers final: 18 residues processed: 123 average time/residue: 0.5406 time to fit residues: 68.8214 Evaluate side-chains 132 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 49 optimal weight: 0.0980 chunk 45 optimal weight: 40.0000 chunk 10 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 36 optimal weight: 7.9990 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 overall best weight: 13.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.130570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114673 restraints weight = 4014.032| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.59 r_work: 0.3521 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4350 Z= 0.235 Angle : 0.671 6.913 5870 Z= 0.374 Chirality : 0.058 0.155 770 Planarity : 0.003 0.012 720 Dihedral : 6.249 19.914 630 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 6.82 % Allowed : 14.55 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 39 PHE 0.017 0.005 PHE G 94 HIS 0.002 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00547 ( 4350) covalent geometry : angle 0.67093 ( 5870) hydrogen bonds : bond 0.02784 ( 95) hydrogen bonds : angle 5.77487 ( 285) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 0.189 Fit side-chains REVERT: A 43 LYS cc_start: 0.8790 (mttt) cc_final: 0.8073 (mptt) REVERT: A 46 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8209 (tmtp) REVERT: A 54 THR cc_start: 0.8312 (OUTLIER) cc_final: 0.7981 (m) REVERT: A 57 GLU cc_start: 0.8706 (tt0) cc_final: 0.8252 (tm-30) REVERT: C 43 LYS cc_start: 0.8710 (mttt) cc_final: 0.7940 (mptt) REVERT: C 46 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8198 (tmtp) REVERT: C 57 GLU cc_start: 0.8731 (tt0) cc_final: 0.8313 (tm-30) REVERT: E 43 LYS cc_start: 0.8656 (mttt) cc_final: 0.7958 (mptt) REVERT: E 57 GLU cc_start: 0.8443 (tt0) cc_final: 0.8017 (tm-30) REVERT: G 43 LYS cc_start: 0.8629 (mttt) cc_final: 0.7938 (mptt) REVERT: G 46 LYS cc_start: 0.8847 (tttt) cc_final: 0.8244 (tmtm) REVERT: I 46 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8257 (tmtm) REVERT: F 43 LYS cc_start: 0.8675 (mttt) cc_final: 0.7955 (mptt) REVERT: F 57 GLU cc_start: 0.8442 (tt0) cc_final: 0.8006 (tm-30) REVERT: J 46 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8165 (tmtm) REVERT: D 43 LYS cc_start: 0.8700 (mttt) cc_final: 0.7946 (mptt) REVERT: D 46 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8237 (tmtp) REVERT: D 57 GLU cc_start: 0.8731 (tt0) cc_final: 0.8314 (tm-30) REVERT: D 83 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7438 (mp0) REVERT: H 43 LYS cc_start: 0.8634 (mttt) cc_final: 0.7967 (mptt) REVERT: H 46 LYS cc_start: 0.8774 (tttt) cc_final: 0.8174 (tmtm) REVERT: B 43 LYS cc_start: 0.8775 (mttt) cc_final: 0.8045 (mptt) REVERT: B 54 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8021 (m) REVERT: B 57 GLU cc_start: 0.8693 (tt0) cc_final: 0.8232 (tm-30) outliers start: 30 outliers final: 18 residues processed: 117 average time/residue: 0.5534 time to fit residues: 66.8730 Evaluate side-chains 133 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 20.0000 chunk 59 optimal weight: 50.0000 chunk 56 optimal weight: 20.0000 chunk 8 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 46 optimal weight: 30.0000 chunk 48 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 19 optimal weight: 8.9990 overall best weight: 8.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.133221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.117504 restraints weight = 3966.666| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.58 r_work: 0.3557 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4350 Z= 0.168 Angle : 0.580 6.097 5870 Z= 0.324 Chirality : 0.056 0.143 770 Planarity : 0.002 0.009 720 Dihedral : 5.844 18.490 630 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 6.14 % Allowed : 15.23 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.64 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR A 39 PHE 0.016 0.004 PHE G 94 HIS 0.002 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 4350) covalent geometry : angle 0.58006 ( 5870) hydrogen bonds : bond 0.02352 ( 95) hydrogen bonds : angle 5.60073 ( 285) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.160 Fit side-chains REVERT: A 43 LYS cc_start: 0.8757 (mttt) cc_final: 0.8058 (mptt) REVERT: A 46 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8194 (tmtp) REVERT: A 54 THR cc_start: 0.8331 (OUTLIER) cc_final: 0.8004 (m) REVERT: A 57 GLU cc_start: 0.8661 (tt0) cc_final: 0.8227 (tm-30) REVERT: C 43 LYS cc_start: 0.8697 (mttt) cc_final: 0.7940 (mptt) REVERT: C 57 GLU cc_start: 0.8741 (tt0) cc_final: 0.8395 (tm-30) REVERT: E 43 LYS cc_start: 0.8628 (mttt) cc_final: 0.7914 (mptt) REVERT: E 57 GLU cc_start: 0.8430 (tt0) cc_final: 0.8094 (tm-30) REVERT: G 43 LYS cc_start: 0.8655 (mttt) cc_final: 0.7991 (mptt) REVERT: G 46 LYS cc_start: 0.8854 (tttt) cc_final: 0.8281 (tmtm) REVERT: I 46 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8291 (tmtm) REVERT: I 57 GLU cc_start: 0.8643 (tt0) cc_final: 0.8276 (tm-30) REVERT: F 43 LYS cc_start: 0.8627 (mttt) cc_final: 0.7895 (mptt) REVERT: F 57 GLU cc_start: 0.8451 (tt0) cc_final: 0.8029 (tm-30) REVERT: J 46 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8195 (tmtm) REVERT: D 43 LYS cc_start: 0.8677 (mttt) cc_final: 0.7945 (mptt) REVERT: D 57 GLU cc_start: 0.8732 (tt0) cc_final: 0.8394 (tm-30) REVERT: D 83 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7367 (mp0) REVERT: H 43 LYS cc_start: 0.8648 (mttt) cc_final: 0.8001 (mptt) REVERT: H 46 LYS cc_start: 0.8783 (tttt) cc_final: 0.8217 (tmtm) REVERT: B 43 LYS cc_start: 0.8756 (mttt) cc_final: 0.8045 (mptt) REVERT: B 54 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.7985 (m) REVERT: B 57 GLU cc_start: 0.8673 (tt0) cc_final: 0.8186 (tm-30) outliers start: 27 outliers final: 19 residues processed: 114 average time/residue: 0.5254 time to fit residues: 61.9570 Evaluate side-chains 130 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 15 optimal weight: 20.0000 chunk 7 optimal weight: 30.0000 chunk 57 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 23 optimal weight: 50.0000 chunk 52 optimal weight: 8.9990 chunk 43 optimal weight: 30.0000 chunk 50 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 3 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.130434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114645 restraints weight = 4011.538| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.59 r_work: 0.3523 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 4350 Z= 0.229 Angle : 0.662 6.626 5870 Z= 0.370 Chirality : 0.058 0.155 770 Planarity : 0.003 0.011 720 Dihedral : 6.215 19.630 630 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 6.36 % Allowed : 15.00 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.33), residues: 610 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.019 0.003 TYR A 39 PHE 0.017 0.004 PHE G 94 HIS 0.003 0.001 HIS F 50 Details of bonding type rmsd covalent geometry : bond 0.00532 ( 4350) covalent geometry : angle 0.66164 ( 5870) hydrogen bonds : bond 0.02746 ( 95) hydrogen bonds : angle 5.73790 ( 285) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1220 Ramachandran restraints generated. 610 Oldfield, 0 Emsley, 610 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 0.176 Fit side-chains REVERT: A 43 LYS cc_start: 0.8767 (mttt) cc_final: 0.8045 (mptt) REVERT: A 46 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8196 (tmtp) REVERT: A 54 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.7977 (m) REVERT: A 57 GLU cc_start: 0.8688 (tt0) cc_final: 0.8239 (tm-30) REVERT: C 43 LYS cc_start: 0.8715 (mttt) cc_final: 0.7927 (mptt) REVERT: C 46 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8198 (tmtp) REVERT: C 57 GLU cc_start: 0.8738 (tt0) cc_final: 0.8333 (tm-30) REVERT: E 43 LYS cc_start: 0.8660 (mttt) cc_final: 0.7936 (mptt) REVERT: E 57 GLU cc_start: 0.8439 (tt0) cc_final: 0.8019 (tm-30) REVERT: G 43 LYS cc_start: 0.8645 (mttt) cc_final: 0.7963 (mptt) REVERT: G 46 LYS cc_start: 0.8848 (tttt) cc_final: 0.8248 (tmtm) REVERT: I 46 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8264 (tmtm) REVERT: I 57 GLU cc_start: 0.8628 (tt0) cc_final: 0.8273 (tm-30) REVERT: F 43 LYS cc_start: 0.8664 (mttt) cc_final: 0.7920 (mptt) REVERT: F 57 GLU cc_start: 0.8435 (tt0) cc_final: 0.8004 (tm-30) REVERT: J 46 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8163 (tmtm) REVERT: D 43 LYS cc_start: 0.8710 (mttt) cc_final: 0.7950 (mptt) REVERT: D 46 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8239 (tmtp) REVERT: D 57 GLU cc_start: 0.8738 (tt0) cc_final: 0.8336 (tm-30) REVERT: D 83 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7352 (mp0) REVERT: H 43 LYS cc_start: 0.8666 (mttt) cc_final: 0.7999 (mptt) REVERT: H 46 LYS cc_start: 0.8774 (tttt) cc_final: 0.8177 (tmtm) REVERT: B 43 LYS cc_start: 0.8750 (mttt) cc_final: 0.8015 (mptt) REVERT: B 54 THR cc_start: 0.8350 (OUTLIER) cc_final: 0.8018 (m) REVERT: B 57 GLU cc_start: 0.8691 (tt0) cc_final: 0.8245 (tm-30) outliers start: 28 outliers final: 18 residues processed: 119 average time/residue: 0.5324 time to fit residues: 65.4145 Evaluate side-chains 132 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 107 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain I residue 46 LYS Chi-restraints excluded: chain I residue 54 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 74 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 54 THR Chi-restraints excluded: chain J residue 75 THR Chi-restraints excluded: chain D residue 46 LYS Chi-restraints excluded: chain D residue 74 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.8359 > 50: distance: 14 - 16: 9.792 distance: 16 - 17: 9.264 distance: 17 - 18: 14.111 distance: 18 - 19: 36.078 distance: 18 - 21: 16.537 distance: 21 - 22: 5.570 distance: 22 - 23: 45.616 distance: 23 - 24: 4.963 distance: 23 - 25: 16.256 distance: 25 - 26: 26.101 distance: 26 - 27: 17.966 distance: 26 - 29: 23.837 distance: 27 - 28: 18.942 distance: 27 - 31: 32.456 distance: 29 - 30: 16.861 distance: 31 - 32: 3.927 distance: 32 - 33: 7.817 distance: 32 - 35: 3.864 distance: 33 - 34: 7.294 distance: 33 - 39: 8.153 distance: 35 - 36: 5.904 distance: 35 - 37: 18.880 distance: 36 - 38: 10.245 distance: 39 - 40: 4.640 distance: 39 - 184: 7.227 distance: 40 - 41: 6.190 distance: 41 - 42: 3.638 distance: 41 - 44: 7.522 distance: 42 - 194: 9.345 distance: 44 - 45: 5.651 distance: 45 - 46: 12.168 distance: 45 - 48: 19.578 distance: 46 - 47: 15.814 distance: 46 - 49: 17.245 distance: 49 - 50: 7.075 distance: 49 - 197: 8.849 distance: 50 - 51: 7.781 distance: 50 - 53: 14.935 distance: 51 - 52: 8.575 distance: 51 - 54: 11.090 distance: 52 - 204: 8.395 distance: 54 - 55: 11.563 distance: 55 - 56: 7.026 distance: 55 - 58: 9.540 distance: 56 - 57: 8.576 distance: 56 - 61: 7.172 distance: 58 - 59: 3.841 distance: 61 - 62: 9.649 distance: 61 - 207: 9.908 distance: 62 - 63: 3.769 distance: 63 - 64: 5.452 distance: 63 - 65: 3.094 distance: 64 - 135: 7.360 distance: 65 - 66: 4.129 distance: 66 - 67: 13.012 distance: 66 - 69: 13.097 distance: 67 - 68: 8.437 distance: 67 - 76: 3.694 distance: 69 - 70: 13.599 distance: 70 - 71: 8.492 distance: 70 - 72: 6.255 distance: 71 - 73: 5.024 distance: 72 - 74: 4.756 distance: 73 - 75: 6.017 distance: 74 - 75: 8.444 distance: 76 - 138: 3.137