Starting phenix.real_space_refine on Wed Mar 4 18:35:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1p_34430/03_2026/8h1p_34430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1p_34430/03_2026/8h1p_34430.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h1p_34430/03_2026/8h1p_34430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1p_34430/03_2026/8h1p_34430.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1p_34430/03_2026/8h1p_34430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1p_34430/03_2026/8h1p_34430.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 9977 2.51 5 N 2871 2.21 5 O 3014 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15950 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K Time building chain proxies: 1.46, per 1000 atoms: 0.09 Number of scatterers: 15950 At special positions: 0 Unit cell: (134.62, 134.62, 76.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 3014 8.00 N 2871 7.00 C 9977 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: 1.43 Conformation dependent library (CDL) restraints added in 643.4 milliseconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3674 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 22 sheets defined 41.9% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE A 166 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'B' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE B 166 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'C' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 Processing helix chain 'C' and resid 134 through 157 removed outlier: 4.032A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE C 166 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE D 166 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 197 through 207 Processing helix chain 'E' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 134 through 157 removed outlier: 4.030A pdb=" N SER E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE E 166 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 197 through 207 Processing helix chain 'F' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE F 166 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 197 through 208 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 Processing helix chain 'G' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE G 166 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'H' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 79 Processing helix chain 'H' and resid 134 through 157 removed outlier: 4.032A pdb=" N SER H 157 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE H 166 " --> pdb=" O GLY H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 177 Processing helix chain 'H' and resid 197 through 207 Processing helix chain 'I' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 Processing helix chain 'I' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE I 166 " --> pdb=" O GLY I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 Processing helix chain 'I' and resid 197 through 207 Processing helix chain 'J' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 79 Processing helix chain 'J' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE J 166 " --> pdb=" O GLY J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 177 Processing helix chain 'J' and resid 197 through 207 Processing helix chain 'K' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN K 45 " --> pdb=" O LYS K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 79 Processing helix chain 'K' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE K 166 " --> pdb=" O GLY K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 177 Processing helix chain 'K' and resid 197 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 99 removed outlier: 5.377A pdb=" N HIS A 86 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN A 114 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 112 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 90 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 106 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 96 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 104 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 98 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS B 86 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN B 114 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG B 112 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 90 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY B 106 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL B 96 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR B 104 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 98 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS C 86 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN C 114 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE C 88 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG C 112 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 90 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY C 106 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 96 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR C 104 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 98 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS D 86 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN D 114 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE D 88 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG D 112 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 90 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY D 106 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL D 96 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR D 104 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D 98 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS E 86 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN E 114 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE E 88 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG E 112 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN E 90 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY E 106 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL E 96 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR E 104 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU E 98 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS F 86 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN F 114 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG F 112 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN F 90 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY F 106 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL F 96 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR F 104 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU F 98 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 52 through 56 Processing sheet with id=AB5, first strand: chain 'G' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS G 86 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN G 114 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE G 88 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG G 112 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN G 90 " --> pdb=" O PHE G 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY G 106 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL G 96 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR G 104 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU G 98 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 52 through 56 Processing sheet with id=AB7, first strand: chain 'H' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS H 86 " --> pdb=" O GLN H 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN H 114 " --> pdb=" O HIS H 86 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE H 88 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG H 112 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN H 90 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY H 106 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL H 96 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR H 104 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU H 98 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 52 through 56 Processing sheet with id=AB9, first strand: chain 'I' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS I 86 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN I 114 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE I 88 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG I 112 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN I 90 " --> pdb=" O PHE I 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY I 106 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL I 96 " --> pdb=" O TYR I 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR I 104 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU I 98 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS I 102 " --> pdb=" O LEU I 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 52 through 56 Processing sheet with id=AC2, first strand: chain 'J' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS J 86 " --> pdb=" O GLN J 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN J 114 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE J 88 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG J 112 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN J 90 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY J 106 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL J 96 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR J 104 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU J 98 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'K' and resid 84 through 99 removed outlier: 5.379A pdb=" N HIS K 86 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN K 114 " --> pdb=" O HIS K 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE K 88 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG K 112 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN K 90 " --> pdb=" O PHE K 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY K 106 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL K 96 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR K 104 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU K 98 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2250 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: 2.22 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5434 1.34 - 1.46: 2510 1.46 - 1.57: 8160 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16214 Sorted by residual: bond pdb=" CB ASN I 100 " pdb=" CG ASN I 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.39e+00 bond pdb=" CB ASN C 100 " pdb=" CG ASN C 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CB ASN H 100 " pdb=" CG ASN H 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CB ASN E 100 " pdb=" CG ASN E 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.34e+00 bond pdb=" CB ASN G 100 " pdb=" CG ASN G 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 20685 1.07 - 2.15: 804 2.15 - 3.22: 247 3.22 - 4.29: 33 4.29 - 5.37: 22 Bond angle restraints: 21791 Sorted by residual: angle pdb=" CA ASN G 100 " pdb=" CB ASN G 100 " pdb=" CG ASN G 100 " ideal model delta sigma weight residual 112.60 115.06 -2.46 1.00e+00 1.00e+00 6.04e+00 angle pdb=" CA ASN B 100 " pdb=" CB ASN B 100 " pdb=" CG ASN B 100 " ideal model delta sigma weight residual 112.60 115.05 -2.45 1.00e+00 1.00e+00 5.99e+00 angle pdb=" CA ASN K 100 " pdb=" CB ASN K 100 " pdb=" CG ASN K 100 " ideal model delta sigma weight residual 112.60 115.03 -2.43 1.00e+00 1.00e+00 5.92e+00 angle pdb=" CA ASN H 100 " pdb=" CB ASN H 100 " pdb=" CG ASN H 100 " ideal model delta sigma weight residual 112.60 115.03 -2.43 1.00e+00 1.00e+00 5.91e+00 angle pdb=" CA ASN J 100 " pdb=" CB ASN J 100 " pdb=" CG ASN J 100 " ideal model delta sigma weight residual 112.60 115.02 -2.42 1.00e+00 1.00e+00 5.88e+00 ... (remaining 21786 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8305 17.94 - 35.88: 1034 35.88 - 53.83: 363 53.83 - 71.77: 55 71.77 - 89.71: 44 Dihedral angle restraints: 9801 sinusoidal: 4004 harmonic: 5797 Sorted by residual: dihedral pdb=" CG ARG F 193 " pdb=" CD ARG F 193 " pdb=" NE ARG F 193 " pdb=" CZ ARG F 193 " ideal model delta sinusoidal sigma weight residual 180.00 135.76 44.24 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG H 193 " pdb=" CD ARG H 193 " pdb=" NE ARG H 193 " pdb=" CZ ARG H 193 " ideal model delta sinusoidal sigma weight residual 180.00 135.77 44.23 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG I 193 " pdb=" CD ARG I 193 " pdb=" NE ARG I 193 " pdb=" CZ ARG I 193 " ideal model delta sinusoidal sigma weight residual 180.00 135.78 44.22 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9798 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1519 0.034 - 0.069: 516 0.069 - 0.103: 187 0.103 - 0.137: 55 0.137 - 0.172: 22 Chirality restraints: 2299 Sorted by residual: chirality pdb=" CA ASP A 149 " pdb=" N ASP A 149 " pdb=" C ASP A 149 " pdb=" CB ASP A 149 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA ASP D 149 " pdb=" N ASP D 149 " pdb=" C ASP D 149 " pdb=" CB ASP D 149 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ASP I 149 " pdb=" N ASP I 149 " pdb=" C ASP I 149 " pdb=" CB ASP I 149 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 2296 not shown) Planarity restraints: 2882 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN K 100 " -0.005 2.00e-02 2.50e+03 1.00e-02 1.01e+00 pdb=" C ASN K 100 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN K 100 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY K 101 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 100 " -0.005 2.00e-02 2.50e+03 9.95e-03 9.89e-01 pdb=" C ASN E 100 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN E 100 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY E 101 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 100 " -0.005 2.00e-02 2.50e+03 9.92e-03 9.83e-01 pdb=" C ASN F 100 " 0.017 2.00e-02 2.50e+03 pdb=" O ASN F 100 " -0.007 2.00e-02 2.50e+03 pdb=" N GLY F 101 " -0.006 2.00e-02 2.50e+03 ... (remaining 2879 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1518 2.75 - 3.29: 15491 3.29 - 3.82: 25801 3.82 - 4.36: 31506 4.36 - 4.90: 55305 Nonbonded interactions: 129621 Sorted by model distance: nonbonded pdb=" NH1 ARG C 204 " pdb=" OH TYR E 36 " model vdw 2.208 3.120 nonbonded pdb=" OD1 ASP J 195 " pdb=" OH TYR K 51 " model vdw 2.223 3.040 nonbonded pdb=" OD1 ASP I 195 " pdb=" OH TYR J 51 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 51 " pdb=" OD1 ASP K 195 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASP G 195 " pdb=" OH TYR H 51 " model vdw 2.248 3.040 ... (remaining 129616 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.250 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16214 Z= 0.128 Angle : 0.559 5.365 21791 Z= 0.314 Chirality : 0.044 0.172 2299 Planarity : 0.003 0.022 2882 Dihedral : 18.453 89.710 6127 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 0.00 % Allowed : 24.18 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.18), residues: 2002 helix: 0.69 (0.18), residues: 770 sheet: 0.54 (0.25), residues: 484 loop : 0.05 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 44 TYR 0.013 0.001 TYR G 126 PHE 0.007 0.001 PHE I 26 TRP 0.005 0.001 TRP K 84 HIS 0.003 0.001 HIS K 86 Details of bonding type rmsd covalent geometry : bond 0.00258 (16214) covalent geometry : angle 0.55942 (21791) hydrogen bonds : bond 0.13063 ( 761) hydrogen bonds : angle 5.29882 ( 2250) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7246 (tttt) cc_final: 0.6274 (tppp) REVERT: B 62 LYS cc_start: 0.7069 (tttt) cc_final: 0.6505 (ttpt) REVERT: B 102 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7020 (mmmm) REVERT: C 62 LYS cc_start: 0.7146 (tttt) cc_final: 0.6380 (mmtp) REVERT: E 62 LYS cc_start: 0.6713 (tttt) cc_final: 0.6477 (tppt) REVERT: E 78 MET cc_start: 0.8655 (tpp) cc_final: 0.8320 (tpp) REVERT: E 199 SER cc_start: 0.7539 (t) cc_final: 0.7214 (p) REVERT: F 199 SER cc_start: 0.7677 (t) cc_final: 0.7420 (p) REVERT: G 56 MET cc_start: 0.6283 (ttm) cc_final: 0.5691 (ttm) REVERT: G 77 GLU cc_start: 0.6755 (pt0) cc_final: 0.6512 (pt0) REVERT: H 67 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7925 (mm-30) REVERT: I 199 SER cc_start: 0.7784 (t) cc_final: 0.7473 (p) REVERT: J 62 LYS cc_start: 0.6858 (tttt) cc_final: 0.6339 (tppt) REVERT: J 67 GLU cc_start: 0.8225 (mm-30) cc_final: 0.8003 (mm-30) REVERT: J 199 SER cc_start: 0.7718 (t) cc_final: 0.7438 (p) REVERT: K 53 SER cc_start: 0.7085 (m) cc_final: 0.6654 (p) REVERT: K 62 LYS cc_start: 0.7161 (tttt) cc_final: 0.6273 (tppp) REVERT: K 199 SER cc_start: 0.7717 (t) cc_final: 0.7425 (p) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1142 time to fit residues: 72.4079 Evaluate side-chains 287 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 86 HIS ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 121 HIS B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 HIS C 73 ASN C 86 HIS C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN D 86 HIS ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 121 HIS E 86 HIS E 99 ASN E 121 HIS F 30 GLN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 121 HIS G 30 GLN G 86 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN H 30 GLN H 86 HIS ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 164 ASN I 30 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 121 HIS I 164 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN K 86 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.170369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.125562 restraints weight = 19410.463| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.44 r_work: 0.3213 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16214 Z= 0.286 Angle : 0.635 5.394 21791 Z= 0.342 Chirality : 0.049 0.305 2299 Planarity : 0.004 0.027 2882 Dihedral : 4.177 15.465 2255 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.09 % Allowed : 20.20 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2002 helix: 0.79 (0.17), residues: 781 sheet: 0.37 (0.24), residues: 495 loop : -0.39 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 193 TYR 0.022 0.002 TYR G 36 PHE 0.016 0.002 PHE I 110 TRP 0.011 0.002 TRP H 84 HIS 0.009 0.002 HIS G 86 Details of bonding type rmsd covalent geometry : bond 0.00653 (16214) covalent geometry : angle 0.63532 (21791) hydrogen bonds : bond 0.04832 ( 761) hydrogen bonds : angle 4.48339 ( 2250) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 381 time to evaluate : 0.618 Fit side-chains REVERT: A 77 GLU cc_start: 0.7513 (pt0) cc_final: 0.7113 (pt0) REVERT: A 139 LEU cc_start: 0.9069 (mm) cc_final: 0.8792 (mm) REVERT: A 195 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7813 (t0) REVERT: B 77 GLU cc_start: 0.7655 (pt0) cc_final: 0.7360 (pt0) REVERT: B 123 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7620 (t70) REVERT: B 139 LEU cc_start: 0.8903 (mm) cc_final: 0.8603 (mm) REVERT: B 195 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7829 (t0) REVERT: C 126 TYR cc_start: 0.8301 (t80) cc_final: 0.8068 (t80) REVERT: C 195 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8009 (t0) REVERT: D 195 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (t0) REVERT: E 97 ASP cc_start: 0.7619 (m-30) cc_final: 0.7382 (m-30) REVERT: E 139 LEU cc_start: 0.9026 (mm) cc_final: 0.8821 (mm) REVERT: F 195 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7430 (t0) REVERT: G 37 GLN cc_start: 0.8463 (mt0) cc_final: 0.8138 (mm-40) REVERT: G 77 GLU cc_start: 0.7321 (pt0) cc_final: 0.7064 (pt0) REVERT: G 126 TYR cc_start: 0.8349 (t80) cc_final: 0.8112 (t80) REVERT: G 195 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7598 (t0) REVERT: H 149 ASP cc_start: 0.8499 (m-30) cc_final: 0.8272 (m-30) REVERT: H 195 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7241 (t0) REVERT: I 77 GLU cc_start: 0.7477 (pt0) cc_final: 0.7256 (pt0) REVERT: I 126 TYR cc_start: 0.8448 (t80) cc_final: 0.8214 (t80) REVERT: J 62 LYS cc_start: 0.6863 (tttt) cc_final: 0.6302 (tppt) REVERT: J 76 ASN cc_start: 0.8114 (m110) cc_final: 0.7901 (m110) REVERT: J 195 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7871 (t0) REVERT: K 62 LYS cc_start: 0.7402 (tttt) cc_final: 0.6543 (tppp) REVERT: K 77 GLU cc_start: 0.7417 (pt0) cc_final: 0.7199 (pt0) REVERT: K 195 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7614 (t0) outliers start: 52 outliers final: 20 residues processed: 411 average time/residue: 0.1097 time to fit residues: 70.0350 Evaluate side-chains 346 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 316 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 195 ASP Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 148 THR Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 195 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 123 optimal weight: 0.0470 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 181 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 125 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.4082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 91 GLN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128818 restraints weight = 19395.721| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.44 r_work: 0.3241 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16214 Z= 0.139 Angle : 0.495 8.033 21791 Z= 0.268 Chirality : 0.044 0.215 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.760 16.475 2255 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.50 % Allowed : 20.86 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.18), residues: 2002 helix: 1.30 (0.18), residues: 781 sheet: 0.90 (0.25), residues: 473 loop : -0.33 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.020 0.001 TYR G 36 PHE 0.010 0.001 PHE J 110 TRP 0.003 0.001 TRP B 84 HIS 0.004 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00320 (16214) covalent geometry : angle 0.49519 (21791) hydrogen bonds : bond 0.03441 ( 761) hydrogen bonds : angle 4.16687 ( 2250) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 195 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7552 (t0) REVERT: B 62 LYS cc_start: 0.7207 (tttt) cc_final: 0.6511 (ttpt) REVERT: B 117 ASP cc_start: 0.8143 (p0) cc_final: 0.7893 (p0) REVERT: B 139 LEU cc_start: 0.8896 (mm) cc_final: 0.8596 (mm) REVERT: B 195 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7655 (t0) REVERT: C 78 MET cc_start: 0.8926 (tpp) cc_final: 0.8498 (tpp) REVERT: C 126 TYR cc_start: 0.8329 (t80) cc_final: 0.7960 (t80) REVERT: C 139 LEU cc_start: 0.8929 (mm) cc_final: 0.8705 (mm) REVERT: C 195 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7887 (t0) REVERT: E 139 LEU cc_start: 0.9013 (mm) cc_final: 0.8800 (mm) REVERT: G 37 GLN cc_start: 0.8438 (mt0) cc_final: 0.8086 (mm-40) REVERT: G 91 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8094 (tt0) REVERT: G 126 TYR cc_start: 0.8319 (t80) cc_final: 0.8060 (t80) REVERT: H 78 MET cc_start: 0.8787 (tpp) cc_final: 0.8486 (tpp) REVERT: H 149 ASP cc_start: 0.8449 (m-30) cc_final: 0.8211 (m-30) REVERT: I 139 LEU cc_start: 0.9094 (mm) cc_final: 0.8879 (mm) REVERT: J 62 LYS cc_start: 0.6859 (tttt) cc_final: 0.6290 (tppt) REVERT: J 195 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7386 (t0) REVERT: K 62 LYS cc_start: 0.7366 (tttt) cc_final: 0.6491 (tppp) REVERT: K 77 GLU cc_start: 0.7423 (pt0) cc_final: 0.7098 (pt0) REVERT: K 197 GLU cc_start: 0.6260 (mt-10) cc_final: 0.6011 (mt-10) outliers start: 42 outliers final: 27 residues processed: 383 average time/residue: 0.1013 time to fit residues: 60.9341 Evaluate side-chains 338 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 306 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 75 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 149 optimal weight: 0.0010 chunk 191 optimal weight: 0.8980 chunk 48 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 overall best weight: 1.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN E 99 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN J 99 ASN K 30 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.128318 restraints weight = 19295.631| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.49 r_work: 0.3275 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16214 Z= 0.122 Angle : 0.475 11.878 21791 Z= 0.257 Chirality : 0.042 0.143 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.620 15.304 2255 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.32 % Allowed : 22.40 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.18), residues: 2002 helix: 1.54 (0.18), residues: 781 sheet: 1.02 (0.25), residues: 473 loop : -0.30 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 44 TYR 0.019 0.001 TYR G 36 PHE 0.009 0.001 PHE B 110 TRP 0.003 0.001 TRP B 84 HIS 0.003 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00277 (16214) covalent geometry : angle 0.47490 (21791) hydrogen bonds : bond 0.03171 ( 761) hydrogen bonds : angle 4.08894 ( 2250) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 348 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8483 (pm20) cc_final: 0.8243 (pm20) REVERT: A 139 LEU cc_start: 0.9056 (mm) cc_final: 0.8763 (mm) REVERT: B 62 LYS cc_start: 0.7490 (tttt) cc_final: 0.6754 (ttpt) REVERT: B 117 ASP cc_start: 0.8216 (p0) cc_final: 0.8012 (p0) REVERT: C 78 MET cc_start: 0.8778 (tpp) cc_final: 0.8457 (tpp) REVERT: C 126 TYR cc_start: 0.8405 (t80) cc_final: 0.8074 (t80) REVERT: C 139 LEU cc_start: 0.8922 (mm) cc_final: 0.8671 (mm) REVERT: C 195 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7715 (t0) REVERT: D 45 GLN cc_start: 0.8479 (pm20) cc_final: 0.8226 (pm20) REVERT: D 62 LYS cc_start: 0.7185 (tttt) cc_final: 0.6561 (tppt) REVERT: E 45 GLN cc_start: 0.8471 (pm20) cc_final: 0.8202 (pm20) REVERT: E 97 ASP cc_start: 0.7590 (m-30) cc_final: 0.7288 (m-30) REVERT: E 139 LEU cc_start: 0.8999 (mm) cc_final: 0.8756 (mm) REVERT: F 117 ASP cc_start: 0.8101 (p0) cc_final: 0.7750 (p0) REVERT: G 37 GLN cc_start: 0.8438 (mt0) cc_final: 0.8097 (mm-40) REVERT: G 91 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7917 (tt0) REVERT: G 126 TYR cc_start: 0.8277 (t80) cc_final: 0.8002 (t80) REVERT: H 62 LYS cc_start: 0.7126 (tttt) cc_final: 0.6502 (tppt) REVERT: H 78 MET cc_start: 0.8720 (tpp) cc_final: 0.8390 (tpp) REVERT: H 149 ASP cc_start: 0.8448 (m-30) cc_final: 0.8161 (m-30) REVERT: J 62 LYS cc_start: 0.6832 (tttt) cc_final: 0.6257 (tppt) REVERT: J 195 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7487 (t70) REVERT: K 62 LYS cc_start: 0.7361 (tttt) cc_final: 0.6503 (tppp) outliers start: 39 outliers final: 25 residues processed: 370 average time/residue: 0.1064 time to fit residues: 61.8528 Evaluate side-chains 310 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 282 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 181 optimal weight: 0.0670 chunk 127 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 chunk 156 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 0.0070 chunk 167 optimal weight: 0.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 99 ASN F 30 GLN F 76 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 91 GLN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 164 ASN J 30 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN K 30 GLN K 99 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.171503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.127167 restraints weight = 19261.070| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.42 r_work: 0.3265 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16214 Z= 0.165 Angle : 0.509 11.978 21791 Z= 0.274 Chirality : 0.043 0.144 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.699 14.920 2255 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.62 % Allowed : 21.69 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2002 helix: 1.50 (0.18), residues: 781 sheet: 0.85 (0.25), residues: 484 loop : -0.40 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 44 TYR 0.023 0.002 TYR G 36 PHE 0.012 0.001 PHE C 110 TRP 0.007 0.001 TRP B 84 HIS 0.005 0.001 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00378 (16214) covalent geometry : angle 0.50857 (21791) hydrogen bonds : bond 0.03575 ( 761) hydrogen bonds : angle 4.15261 ( 2250) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 0.498 Fit side-chains REVERT: A 45 GLN cc_start: 0.8431 (pm20) cc_final: 0.8131 (pm20) REVERT: A 139 LEU cc_start: 0.9092 (mm) cc_final: 0.8809 (mm) REVERT: B 62 LYS cc_start: 0.7524 (tttt) cc_final: 0.6804 (ttpt) REVERT: B 175 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7158 (mt) REVERT: C 78 MET cc_start: 0.8826 (tpp) cc_final: 0.8587 (tpp) REVERT: C 126 TYR cc_start: 0.8366 (t80) cc_final: 0.8088 (t80) REVERT: C 139 LEU cc_start: 0.8972 (mm) cc_final: 0.8712 (mm) REVERT: D 45 GLN cc_start: 0.8437 (pm20) cc_final: 0.8165 (pm20) REVERT: D 62 LYS cc_start: 0.7082 (tttt) cc_final: 0.6359 (tppt) REVERT: E 45 GLN cc_start: 0.8548 (pm20) cc_final: 0.8302 (pm20) REVERT: E 97 ASP cc_start: 0.7627 (m-30) cc_final: 0.7357 (m-30) REVERT: E 139 LEU cc_start: 0.8992 (mm) cc_final: 0.8757 (mm) REVERT: F 45 GLN cc_start: 0.8336 (pm20) cc_final: 0.8126 (pm20) REVERT: F 117 ASP cc_start: 0.8168 (p0) cc_final: 0.7942 (p0) REVERT: F 171 TYR cc_start: 0.7040 (t80) cc_final: 0.6747 (t80) REVERT: F 192 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7249 (tppt) REVERT: G 37 GLN cc_start: 0.8463 (mt0) cc_final: 0.8112 (mm-40) REVERT: G 91 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8151 (tt0) REVERT: G 97 ASP cc_start: 0.7555 (m-30) cc_final: 0.7343 (m-30) REVERT: G 126 TYR cc_start: 0.8340 (t80) cc_final: 0.8127 (t80) REVERT: G 139 LEU cc_start: 0.8887 (mm) cc_final: 0.8482 (mm) REVERT: H 62 LYS cc_start: 0.7120 (tttt) cc_final: 0.6483 (tppt) REVERT: H 78 MET cc_start: 0.8793 (tpp) cc_final: 0.8494 (tpp) REVERT: H 149 ASP cc_start: 0.8535 (m-30) cc_final: 0.8238 (m-30) REVERT: I 37 GLN cc_start: 0.8232 (mt0) cc_final: 0.7907 (mm-40) REVERT: J 62 LYS cc_start: 0.6769 (tttt) cc_final: 0.6230 (tppt) REVERT: J 195 ASP cc_start: 0.7949 (OUTLIER) cc_final: 0.7463 (t0) REVERT: K 62 LYS cc_start: 0.7245 (tttt) cc_final: 0.6594 (tppp) REVERT: K 77 GLU cc_start: 0.7420 (pt0) cc_final: 0.6940 (pt0) outliers start: 61 outliers final: 32 residues processed: 351 average time/residue: 0.1027 time to fit residues: 56.6770 Evaluate side-chains 324 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 288 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 192 LYS Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 164 ASN Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 40.0000 chunk 28 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 183 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 chunk 187 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN D 99 ASN E 99 ASN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** G 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 164 ASN J 30 GLN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN K 30 GLN K 99 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.127987 restraints weight = 19149.003| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.41 r_work: 0.3263 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16214 Z= 0.162 Angle : 0.510 12.360 21791 Z= 0.274 Chirality : 0.044 0.240 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.731 14.389 2255 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.73 % Allowed : 22.52 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.18), residues: 2002 helix: 1.51 (0.18), residues: 781 sheet: 0.87 (0.25), residues: 484 loop : -0.43 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 44 TYR 0.024 0.002 TYR G 36 PHE 0.012 0.001 PHE I 110 TRP 0.005 0.001 TRP B 84 HIS 0.005 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00374 (16214) covalent geometry : angle 0.51026 (21791) hydrogen bonds : bond 0.03548 ( 761) hydrogen bonds : angle 4.11669 ( 2250) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 322 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8448 (pm20) cc_final: 0.7535 (pm20) REVERT: A 139 LEU cc_start: 0.9069 (mm) cc_final: 0.8806 (mm) REVERT: B 62 LYS cc_start: 0.7557 (tttt) cc_final: 0.6578 (tppp) REVERT: B 175 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7233 (mt) REVERT: C 78 MET cc_start: 0.8829 (tpp) cc_final: 0.8592 (tpp) REVERT: C 126 TYR cc_start: 0.8443 (t80) cc_final: 0.8169 (t80) REVERT: C 139 LEU cc_start: 0.8968 (mm) cc_final: 0.8716 (mm) REVERT: C 171 TYR cc_start: 0.6734 (t80) cc_final: 0.6327 (t80) REVERT: D 45 GLN cc_start: 0.8464 (pm20) cc_final: 0.8132 (pm20) REVERT: D 62 LYS cc_start: 0.6984 (tttt) cc_final: 0.6315 (tppt) REVERT: E 97 ASP cc_start: 0.7631 (m-30) cc_final: 0.7361 (m-30) REVERT: E 139 LEU cc_start: 0.8989 (mm) cc_final: 0.8769 (mm) REVERT: F 45 GLN cc_start: 0.8368 (pm20) cc_final: 0.8123 (pm20) REVERT: F 171 TYR cc_start: 0.7032 (t80) cc_final: 0.6760 (t80) REVERT: G 37 GLN cc_start: 0.8456 (mt0) cc_final: 0.8109 (mm-40) REVERT: G 62 LYS cc_start: 0.6721 (tttt) cc_final: 0.6089 (tppt) REVERT: G 91 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7940 (tt0) REVERT: G 97 ASP cc_start: 0.7583 (m-30) cc_final: 0.7381 (m-30) REVERT: G 126 TYR cc_start: 0.8327 (t80) cc_final: 0.8121 (t80) REVERT: G 139 LEU cc_start: 0.8886 (mm) cc_final: 0.8483 (mm) REVERT: H 78 MET cc_start: 0.8802 (tpp) cc_final: 0.8501 (tpp) REVERT: H 97 ASP cc_start: 0.7378 (m-30) cc_final: 0.7164 (m-30) REVERT: H 149 ASP cc_start: 0.8527 (m-30) cc_final: 0.8234 (m-30) REVERT: J 62 LYS cc_start: 0.6726 (tttt) cc_final: 0.6190 (tppt) REVERT: J 195 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.7753 (t70) REVERT: K 62 LYS cc_start: 0.7219 (tttt) cc_final: 0.6590 (tppp) outliers start: 46 outliers final: 35 residues processed: 347 average time/residue: 0.1058 time to fit residues: 57.5353 Evaluate side-chains 325 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 287 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 164 ASN Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 164 ASN Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 129 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 107 optimal weight: 0.0570 chunk 196 optimal weight: 0.0870 chunk 193 optimal weight: 3.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 164 ASN D 99 ASN E 99 ASN F 30 GLN ** F 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 91 GLN G 99 ASN H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN J 164 ASN K 30 GLN K 99 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.171948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.127766 restraints weight = 19152.175| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.42 r_work: 0.3220 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16214 Z= 0.135 Angle : 0.497 12.793 21791 Z= 0.267 Chirality : 0.044 0.215 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.671 13.884 2255 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.61 % Allowed : 22.82 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2002 helix: 1.57 (0.18), residues: 781 sheet: 0.91 (0.25), residues: 484 loop : -0.36 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 143 TYR 0.022 0.001 TYR G 36 PHE 0.010 0.001 PHE I 110 TRP 0.004 0.001 TRP B 84 HIS 0.004 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00309 (16214) covalent geometry : angle 0.49690 (21791) hydrogen bonds : bond 0.03329 ( 761) hydrogen bonds : angle 4.07419 ( 2250) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9072 (mm) cc_final: 0.8802 (mm) REVERT: B 62 LYS cc_start: 0.7515 (tttt) cc_final: 0.6567 (tppp) REVERT: B 175 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7258 (mt) REVERT: C 126 TYR cc_start: 0.8462 (t80) cc_final: 0.8192 (t80) REVERT: C 139 LEU cc_start: 0.9001 (mm) cc_final: 0.8745 (mm) REVERT: C 171 TYR cc_start: 0.6798 (t80) cc_final: 0.6407 (t80) REVERT: D 62 LYS cc_start: 0.6991 (tttt) cc_final: 0.6330 (tppt) REVERT: E 97 ASP cc_start: 0.7586 (m-30) cc_final: 0.7324 (m-30) REVERT: E 139 LEU cc_start: 0.8995 (mm) cc_final: 0.8774 (mm) REVERT: F 45 GLN cc_start: 0.8354 (pm20) cc_final: 0.8089 (pm20) REVERT: F 171 TYR cc_start: 0.7029 (t80) cc_final: 0.6811 (t80) REVERT: G 37 GLN cc_start: 0.8446 (mt0) cc_final: 0.7256 (mm-40) REVERT: G 62 LYS cc_start: 0.6720 (tttt) cc_final: 0.6098 (tppt) REVERT: G 91 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8141 (tt0) REVERT: G 139 LEU cc_start: 0.8902 (mm) cc_final: 0.8505 (mm) REVERT: H 62 LYS cc_start: 0.7159 (tttt) cc_final: 0.6529 (tptt) REVERT: H 78 MET cc_start: 0.8872 (tpp) cc_final: 0.8583 (tpp) REVERT: H 149 ASP cc_start: 0.8573 (m-30) cc_final: 0.8278 (m-30) REVERT: J 62 LYS cc_start: 0.6691 (tttt) cc_final: 0.6159 (tppt) REVERT: K 62 LYS cc_start: 0.7234 (tttt) cc_final: 0.6640 (tppp) outliers start: 44 outliers final: 32 residues processed: 335 average time/residue: 0.1046 time to fit residues: 55.7507 Evaluate side-chains 323 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 289 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 36 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 50.0000 chunk 136 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN D 99 ASN E 30 GLN E 99 ASN F 76 ASN F 86 HIS ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN G 121 HIS H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.168071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.123508 restraints weight = 19470.623| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.42 r_work: 0.3197 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16214 Z= 0.286 Angle : 0.626 12.997 21791 Z= 0.336 Chirality : 0.049 0.298 2299 Planarity : 0.004 0.024 2882 Dihedral : 4.178 18.931 2255 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.32 % Allowed : 22.64 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.18), residues: 2002 helix: 1.20 (0.18), residues: 781 sheet: 0.55 (0.25), residues: 484 loop : -0.76 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 193 TYR 0.031 0.002 TYR G 36 PHE 0.016 0.002 PHE I 110 TRP 0.012 0.003 TRP D 84 HIS 0.011 0.002 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00656 (16214) covalent geometry : angle 0.62582 (21791) hydrogen bonds : bond 0.04669 ( 761) hydrogen bonds : angle 4.34541 ( 2250) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 295 time to evaluate : 0.401 Fit side-chains REVERT: A 45 GLN cc_start: 0.8492 (pm20) cc_final: 0.8155 (pm20) REVERT: A 207 SER cc_start: 0.8272 (t) cc_final: 0.8069 (p) REVERT: B 62 LYS cc_start: 0.7445 (tttt) cc_final: 0.6572 (tppp) REVERT: B 123 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7598 (t70) REVERT: B 139 LEU cc_start: 0.8817 (mm) cc_final: 0.8567 (mm) REVERT: B 175 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7319 (mt) REVERT: C 139 LEU cc_start: 0.9000 (mm) cc_final: 0.8771 (mm) REVERT: C 171 TYR cc_start: 0.6993 (t80) cc_final: 0.6777 (t80) REVERT: C 196 LEU cc_start: 0.7895 (tp) cc_final: 0.7655 (tp) REVERT: D 62 LYS cc_start: 0.6922 (tttt) cc_final: 0.6241 (tppt) REVERT: E 97 ASP cc_start: 0.7709 (m-30) cc_final: 0.7460 (m-30) REVERT: E 139 LEU cc_start: 0.9035 (mm) cc_final: 0.8823 (mm) REVERT: F 45 GLN cc_start: 0.8454 (pm20) cc_final: 0.8223 (pm20) REVERT: F 117 ASP cc_start: 0.8183 (p0) cc_final: 0.7920 (p0) REVERT: F 171 TYR cc_start: 0.7151 (t80) cc_final: 0.6918 (t80) REVERT: G 37 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8188 (mm-40) REVERT: G 62 LYS cc_start: 0.6883 (tttt) cc_final: 0.6381 (tppt) REVERT: G 91 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8137 (tt0) REVERT: G 139 LEU cc_start: 0.8962 (mm) cc_final: 0.8564 (mm) REVERT: H 36 TYR cc_start: 0.8056 (t80) cc_final: 0.7808 (t80) REVERT: H 149 ASP cc_start: 0.8587 (m-30) cc_final: 0.8352 (m-30) REVERT: J 62 LYS cc_start: 0.6677 (tttt) cc_final: 0.6186 (tppt) REVERT: K 62 LYS cc_start: 0.7314 (tttt) cc_final: 0.6594 (tppp) outliers start: 39 outliers final: 30 residues processed: 317 average time/residue: 0.1049 time to fit residues: 52.0774 Evaluate side-chains 304 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 70 optimal weight: 10.0000 chunk 184 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN E 99 ASN F 30 GLN F 76 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 91 GLN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN J 99 ASN J 164 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.172060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128050 restraints weight = 19258.047| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.42 r_work: 0.3207 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16214 Z= 0.155 Angle : 0.525 12.854 21791 Z= 0.283 Chirality : 0.045 0.218 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.879 18.584 2255 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.32 % Allowed : 22.70 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.18), residues: 2002 helix: 1.39 (0.18), residues: 781 sheet: 0.66 (0.25), residues: 484 loop : -0.56 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 44 TYR 0.027 0.002 TYR D 171 PHE 0.012 0.001 PHE I 110 TRP 0.004 0.001 TRP B 84 HIS 0.005 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00356 (16214) covalent geometry : angle 0.52494 (21791) hydrogen bonds : bond 0.03520 ( 761) hydrogen bonds : angle 4.09216 ( 2250) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 305 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9087 (mm) cc_final: 0.8828 (mm) REVERT: B 62 LYS cc_start: 0.7366 (tttt) cc_final: 0.6500 (tppp) REVERT: B 97 ASP cc_start: 0.7635 (m-30) cc_final: 0.7421 (m-30) REVERT: B 117 ASP cc_start: 0.8103 (p0) cc_final: 0.7892 (p0) REVERT: C 78 MET cc_start: 0.8835 (tpp) cc_final: 0.8448 (tpp) REVERT: C 126 TYR cc_start: 0.8306 (t80) cc_final: 0.8020 (t80) REVERT: C 139 LEU cc_start: 0.9009 (mm) cc_final: 0.8753 (mm) REVERT: C 196 LEU cc_start: 0.7714 (tp) cc_final: 0.7472 (tp) REVERT: D 62 LYS cc_start: 0.7002 (tttt) cc_final: 0.6299 (tppt) REVERT: D 78 MET cc_start: 0.8766 (tpp) cc_final: 0.8410 (mmm) REVERT: E 97 ASP cc_start: 0.7719 (m-30) cc_final: 0.7466 (m-30) REVERT: E 139 LEU cc_start: 0.9027 (mm) cc_final: 0.8806 (mm) REVERT: F 45 GLN cc_start: 0.8452 (pm20) cc_final: 0.8158 (pm20) REVERT: F 117 ASP cc_start: 0.8119 (p0) cc_final: 0.7843 (p0) REVERT: G 37 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8167 (mm-40) REVERT: G 45 GLN cc_start: 0.8361 (pm20) cc_final: 0.8036 (pm20) REVERT: G 62 LYS cc_start: 0.6810 (tttt) cc_final: 0.6347 (tppt) REVERT: G 91 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: G 139 LEU cc_start: 0.8930 (mm) cc_final: 0.8515 (mm) REVERT: H 62 LYS cc_start: 0.7324 (tttt) cc_final: 0.6722 (tppt) REVERT: H 149 ASP cc_start: 0.8598 (m-30) cc_final: 0.8349 (m-30) REVERT: I 139 LEU cc_start: 0.9125 (mm) cc_final: 0.8906 (mm) REVERT: J 62 LYS cc_start: 0.6557 (tttt) cc_final: 0.6090 (tppt) REVERT: K 62 LYS cc_start: 0.7262 (tttt) cc_final: 0.6532 (tppp) outliers start: 39 outliers final: 29 residues processed: 328 average time/residue: 0.1035 time to fit residues: 54.2878 Evaluate side-chains 314 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 284 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 2 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 24 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 179 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 91 GLN G 99 ASN H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 164 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.172482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128563 restraints weight = 19279.320| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.40 r_work: 0.3245 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16214 Z= 0.149 Angle : 0.529 13.433 21791 Z= 0.285 Chirality : 0.045 0.195 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.811 18.682 2255 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.02 % Allowed : 23.35 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.19), residues: 2002 helix: 1.45 (0.18), residues: 781 sheet: 0.47 (0.25), residues: 506 loop : -0.45 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 46 TYR 0.036 0.002 TYR F 171 PHE 0.012 0.001 PHE I 110 TRP 0.004 0.001 TRP D 84 HIS 0.004 0.001 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.00343 (16214) covalent geometry : angle 0.52888 (21791) hydrogen bonds : bond 0.03546 ( 761) hydrogen bonds : angle 4.11926 ( 2250) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 300 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9083 (mm) cc_final: 0.8820 (mm) REVERT: B 62 LYS cc_start: 0.7342 (tttt) cc_final: 0.6477 (tppp) REVERT: B 97 ASP cc_start: 0.7619 (m-30) cc_final: 0.7404 (m-30) REVERT: B 117 ASP cc_start: 0.8120 (p0) cc_final: 0.7886 (p0) REVERT: C 78 MET cc_start: 0.8809 (tpp) cc_final: 0.8415 (tpp) REVERT: C 126 TYR cc_start: 0.8299 (t80) cc_final: 0.8033 (t80) REVERT: C 139 LEU cc_start: 0.9000 (mm) cc_final: 0.8740 (mm) REVERT: C 171 TYR cc_start: 0.6784 (t80) cc_final: 0.6349 (t80) REVERT: C 196 LEU cc_start: 0.7796 (tp) cc_final: 0.7576 (tp) REVERT: D 62 LYS cc_start: 0.6998 (tttt) cc_final: 0.6292 (tppt) REVERT: D 78 MET cc_start: 0.8774 (tpp) cc_final: 0.8412 (mmm) REVERT: E 91 GLN cc_start: 0.8643 (tt0) cc_final: 0.8322 (tt0) REVERT: E 97 ASP cc_start: 0.7712 (m-30) cc_final: 0.7475 (m-30) REVERT: E 139 LEU cc_start: 0.9009 (mm) cc_final: 0.8794 (mm) REVERT: F 117 ASP cc_start: 0.8125 (p0) cc_final: 0.7830 (p0) REVERT: G 37 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8112 (mm-40) REVERT: G 45 GLN cc_start: 0.8363 (pm20) cc_final: 0.8120 (pm20) REVERT: G 62 LYS cc_start: 0.6826 (tttt) cc_final: 0.6255 (tppt) REVERT: G 91 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: G 139 LEU cc_start: 0.8936 (mm) cc_final: 0.8530 (mm) REVERT: H 62 LYS cc_start: 0.7316 (tttt) cc_final: 0.6731 (tppt) REVERT: H 149 ASP cc_start: 0.8557 (m-30) cc_final: 0.8306 (m-30) REVERT: I 139 LEU cc_start: 0.9117 (mm) cc_final: 0.8894 (mm) REVERT: J 62 LYS cc_start: 0.6625 (tttt) cc_final: 0.6172 (tppt) REVERT: K 62 LYS cc_start: 0.7147 (tttt) cc_final: 0.6446 (tppp) outliers start: 34 outliers final: 31 residues processed: 319 average time/residue: 0.1016 time to fit residues: 51.7550 Evaluate side-chains 320 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 288 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 50 GLU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 13 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 118 optimal weight: 8.9990 chunk 95 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 2 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 91 GLN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN J 164 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.172609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.128658 restraints weight = 19024.000| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.41 r_work: 0.3214 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16214 Z= 0.146 Angle : 0.524 13.458 21791 Z= 0.284 Chirality : 0.045 0.179 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.777 18.475 2255 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.20 % Allowed : 23.29 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 2002 helix: 1.47 (0.18), residues: 781 sheet: 0.47 (0.24), residues: 506 loop : -0.41 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 44 TYR 0.035 0.002 TYR F 171 PHE 0.011 0.001 PHE C 110 TRP 0.004 0.001 TRP D 84 HIS 0.004 0.001 HIS J 121 Details of bonding type rmsd covalent geometry : bond 0.00334 (16214) covalent geometry : angle 0.52414 (21791) hydrogen bonds : bond 0.03486 ( 761) hydrogen bonds : angle 4.10299 ( 2250) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3217.70 seconds wall clock time: 56 minutes 0.82 seconds (3360.82 seconds total)