Starting phenix.real_space_refine on Sat May 17 10:04:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1p_34430/05_2025/8h1p_34430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1p_34430/05_2025/8h1p_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_34430/05_2025/8h1p_34430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1p_34430/05_2025/8h1p_34430.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1p_34430/05_2025/8h1p_34430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1p_34430/05_2025/8h1p_34430.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 4.17, per 1000 atoms: 0.26 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: 4.16 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.78 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: 4.39 Time building geometry restraints manager: 4.79 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.890 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.005 0.001 TRP K 84 HIS 0.003 0.001 HIS K 86 PHE 0.007 0.001 PHE I 26 TYR 0.013 0.001 TYR G 126 ARG 0.002 0.000 ARG D 44 Details of bonding type rmsd hydrogen bonds : bond 0.13063 ( 761) hydrogen bonds : angle 5.29882 ( 2250) covalent geometry : bond 0.00258 (16214) covalent geometry : angle 0.55942 (21791) *********************** 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 : 1.712 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7246 (tttt) cc_final: 0.6273 (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: 0.6712 (tttt) cc_final: 0.6476 (tppt) REVERT: E 78 MET cc_start: 0.8655 (tpp) cc_final: 0.8321 (tpp) REVERT: E 199 SER cc_start: 0.7540 (t) cc_final: 0.7215 (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: 0.6756 (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: 0.7785 (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: 0.8224 (mm-30) cc_final: 0.8003 (mm-30) REVERT: J 199 SER cc_start: 0.7718 (t) cc_final: 0.7439 (p) REVERT: K 53 SER cc_start: 0.7085 (m) cc_final: 0.6655 (p) REVERT: K 62 LYS cc_start: 0.7160 (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: 0.2518 time to fit residues: 157.0171 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 : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 51 optimal weight: 30.0000 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 179 optimal weight: 9.9990 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 73 ASN ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS E 99 ASN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 GLN F 86 HIS ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN F 121 HIS G 30 GLN G 86 HIS G 91 GLN G 121 HIS G 164 ASN H 30 GLN H 86 HIS H 91 GLN H 121 HIS H 164 ASN I 30 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN I 121 HIS ** 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 ** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.176371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131449 restraints weight = 19394.571| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.48 r_work: 0.3295 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16214 Z= 0.165 Angle : 0.529 5.207 21791 Z= 0.287 Chirality : 0.046 0.253 2299 Planarity : 0.003 0.026 2882 Dihedral : 3.726 13.808 2255 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.97 % Allowed : 18.84 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2002 helix: 1.14 (0.18), residues: 770 sheet: 0.80 (0.25), residues: 484 loop : -0.08 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 84 HIS 0.005 0.001 HIS G 86 PHE 0.013 0.001 PHE I 110 TYR 0.017 0.001 TYR G 36 ARG 0.002 0.000 ARG E 193 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 761) hydrogen bonds : angle 4.27361 ( 2250) covalent geometry : bond 0.00379 (16214) covalent geometry : angle 0.52946 (21791) *********************** 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 410 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 360 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 52 ILE cc_start: 0.7514 (mp) cc_final: 0.7187 (mp) REVERT: A 62 LYS cc_start: 0.7406 (tttt) cc_final: 0.6363 (tppp) REVERT: A 139 LEU cc_start: 0.9017 (mm) cc_final: 0.8781 (mm) REVERT: A 195 ASP cc_start: 0.8078 (OUTLIER) cc_final: 0.7564 (t0) REVERT: B 62 LYS cc_start: 0.7205 (tttt) cc_final: 0.6465 (ttpt) REVERT: B 117 ASP cc_start: 0.8279 (p0) cc_final: 0.8001 (p0) REVERT: B 195 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7651 (t0) REVERT: C 126 TYR cc_start: 0.8331 (t80) cc_final: 0.8081 (t80) REVERT: C 195 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7903 (t0) REVERT: D 139 LEU cc_start: 0.8898 (mm) cc_final: 0.8693 (mm) REVERT: E 149 ASP cc_start: 0.8386 (m-30) cc_final: 0.8181 (m-30) REVERT: F 97 ASP cc_start: 0.7313 (m-30) cc_final: 0.7095 (m-30) REVERT: F 139 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8692 (mm) REVERT: F 195 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7490 (t0) REVERT: G 37 GLN cc_start: 0.8495 (mt0) cc_final: 0.8152 (mm-40) REVERT: H 91 GLN cc_start: 0.8442 (tt0) cc_final: 0.8221 (tt0) REVERT: H 126 TYR cc_start: 0.8346 (t80) cc_final: 0.8113 (t80) REVERT: H 195 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7471 (t0) REVERT: I 77 GLU cc_start: 0.7031 (pt0) cc_final: 0.6698 (pt0) REVERT: I 195 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7711 (t0) REVERT: J 62 LYS cc_start: 0.6921 (tttt) cc_final: 0.6331 (tppt) REVERT: J 195 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7662 (t0) REVERT: K 62 LYS cc_start: 0.7297 (tttt) cc_final: 0.6500 (tppp) REVERT: K 78 MET cc_start: 0.8909 (tpp) cc_final: 0.8664 (tpp) REVERT: K 195 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7898 (t0) outliers start: 50 outliers final: 16 residues processed: 389 average time/residue: 0.2434 time to fit residues: 144.5954 Evaluate side-chains 323 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 298 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ASP 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 195 ASP Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 123 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 166 ILE Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 166 ILE 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 182 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 197 optimal weight: 0.0470 chunk 54 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 140 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.6882 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 91 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 86 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.177836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.133071 restraints weight = 18978.648| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.45 r_work: 0.3284 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16214 Z= 0.105 Angle : 0.461 8.229 21791 Z= 0.250 Chirality : 0.043 0.211 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.509 15.551 2255 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.73 % Allowed : 19.37 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.19), residues: 2002 helix: 1.39 (0.18), residues: 792 sheet: 1.16 (0.26), residues: 473 loop : -0.17 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 84 HIS 0.003 0.001 HIS A 86 PHE 0.008 0.001 PHE D 110 TYR 0.017 0.001 TYR A 171 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.02943 ( 761) hydrogen bonds : angle 4.08358 ( 2250) covalent geometry : bond 0.00236 (16214) covalent geometry : angle 0.46069 (21791) *********************** 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 412 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 366 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7346 (tttt) cc_final: 0.6361 (tppp) REVERT: A 195 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7573 (t0) REVERT: B 62 LYS cc_start: 0.7322 (tttt) cc_final: 0.6603 (ttpt) REVERT: B 78 MET cc_start: 0.8724 (tpp) cc_final: 0.8520 (tpp) REVERT: B 117 ASP cc_start: 0.8254 (p0) cc_final: 0.8036 (p0) REVERT: B 139 LEU cc_start: 0.8884 (mm) cc_final: 0.8577 (mm) REVERT: C 45 GLN cc_start: 0.8434 (pm20) cc_final: 0.8058 (pm20) REVERT: C 78 MET cc_start: 0.8876 (tpp) cc_final: 0.8374 (tpp) REVERT: C 126 TYR cc_start: 0.8302 (t80) cc_final: 0.7977 (t80) REVERT: C 139 LEU cc_start: 0.8916 (mm) cc_final: 0.8690 (mm) REVERT: C 195 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7666 (t0) REVERT: D 55 ARG cc_start: 0.6683 (mtp180) cc_final: 0.6477 (mtm180) REVERT: D 64 CYS cc_start: 0.8574 (t) cc_final: 0.8325 (t) REVERT: E 139 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8798 (mm) REVERT: F 97 ASP cc_start: 0.7366 (m-30) cc_final: 0.7149 (m-30) REVERT: F 139 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8709 (mm) REVERT: G 37 GLN cc_start: 0.8422 (mt0) cc_final: 0.8088 (mm-40) REVERT: G 139 LEU cc_start: 0.8738 (mm) cc_final: 0.8289 (mm) REVERT: G 145 GLU cc_start: 0.8017 (tt0) cc_final: 0.7803 (tt0) REVERT: H 126 TYR cc_start: 0.8378 (t80) cc_final: 0.8101 (t80) REVERT: I 195 ASP cc_start: 0.8043 (OUTLIER) cc_final: 0.7839 (t0) REVERT: J 62 LYS cc_start: 0.6796 (tttt) cc_final: 0.6266 (tppt) REVERT: K 45 GLN cc_start: 0.8361 (pm20) cc_final: 0.7529 (pm20) REVERT: K 62 LYS cc_start: 0.7346 (tttt) cc_final: 0.6584 (tppp) REVERT: K 78 MET cc_start: 0.8868 (tpp) cc_final: 0.8588 (tpp) REVERT: K 139 LEU cc_start: 0.9053 (mm) cc_final: 0.8839 (mm) outliers start: 46 outliers final: 22 residues processed: 392 average time/residue: 0.2442 time to fit residues: 147.3682 Evaluate side-chains 313 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 286 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 C residue 89 THR 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 E residue 139 LEU 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 G residue 89 THR 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 I residue 195 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 10.0000 chunk 192 optimal weight: 0.6980 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 139 optimal weight: 0.4980 chunk 96 optimal weight: 5.9990 chunk 82 optimal weight: 10.0000 chunk 3 optimal weight: 7.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 121 HIS E 76 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 121 HIS ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN ** G 91 GLN ** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 86 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.171955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127231 restraints weight = 19091.979| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.39 r_work: 0.3270 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16214 Z= 0.178 Angle : 0.529 11.452 21791 Z= 0.285 Chirality : 0.044 0.162 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.705 15.662 2255 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.67 % Allowed : 20.56 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.18), residues: 2002 helix: 1.45 (0.18), residues: 781 sheet: 0.91 (0.25), residues: 484 loop : -0.32 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 84 HIS 0.005 0.001 HIS K 86 PHE 0.015 0.002 PHE J 110 TYR 0.021 0.002 TYR G 36 ARG 0.002 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 761) hydrogen bonds : angle 4.21895 ( 2250) covalent geometry : bond 0.00408 (16214) covalent geometry : angle 0.52877 (21791) *********************** 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 358 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 313 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7295 (tttt) cc_final: 0.6319 (tppp) REVERT: A 195 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7775 (t0) REVERT: B 37 GLN cc_start: 0.8463 (mt0) cc_final: 0.8263 (mm-40) REVERT: B 62 LYS cc_start: 0.7518 (tttt) cc_final: 0.6795 (ttpt) REVERT: B 78 MET cc_start: 0.8660 (tpp) cc_final: 0.8251 (tpp) REVERT: B 117 ASP cc_start: 0.8330 (p0) cc_final: 0.8062 (p0) REVERT: C 78 MET cc_start: 0.8813 (tpp) cc_final: 0.8578 (tpp) REVERT: C 126 TYR cc_start: 0.8303 (t80) cc_final: 0.7973 (t80) REVERT: C 139 LEU cc_start: 0.8926 (mm) cc_final: 0.8719 (mm) REVERT: C 171 TYR cc_start: 0.6889 (t80) cc_final: 0.6575 (t80) REVERT: D 45 GLN cc_start: 0.8529 (pm20) cc_final: 0.8157 (pm20) REVERT: D 62 LYS cc_start: 0.7132 (tttt) cc_final: 0.6496 (tppt) REVERT: E 45 GLN cc_start: 0.8527 (pm20) cc_final: 0.8322 (pm20) REVERT: E 97 ASP cc_start: 0.7642 (m-30) cc_final: 0.7385 (m-30) REVERT: E 139 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8759 (mm) REVERT: F 97 ASP cc_start: 0.7460 (m-30) cc_final: 0.7259 (m-30) REVERT: G 37 GLN cc_start: 0.8468 (mt0) cc_final: 0.8133 (mm-40) REVERT: J 62 LYS cc_start: 0.6774 (tttt) cc_final: 0.6248 (tppt) REVERT: J 76 ASN cc_start: 0.8268 (m110) cc_final: 0.8064 (m110) REVERT: K 62 LYS cc_start: 0.7305 (tttt) cc_final: 0.6478 (tppp) outliers start: 45 outliers final: 22 residues processed: 343 average time/residue: 0.2289 time to fit residues: 122.6764 Evaluate side-chains 300 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 32 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 89 THR 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 K residue 89 THR 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 124 optimal weight: 0.4980 chunk 197 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 193 optimal weight: 0.0170 chunk 52 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.0818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 30 GLN ** G 91 GLN ** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN K 30 GLN ** K 86 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.173802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129522 restraints weight = 19334.201| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.42 r_work: 0.3245 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16214 Z= 0.117 Angle : 0.476 12.000 21791 Z= 0.256 Chirality : 0.043 0.221 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.575 14.301 2255 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.32 % Allowed : 21.15 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2002 helix: 1.73 (0.18), residues: 770 sheet: 1.00 (0.25), residues: 484 loop : -0.24 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 84 HIS 0.003 0.001 HIS B 86 PHE 0.009 0.001 PHE B 110 TYR 0.020 0.001 TYR G 36 ARG 0.002 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.03068 ( 761) hydrogen bonds : angle 4.05501 ( 2250) covalent geometry : bond 0.00266 (16214) covalent geometry : angle 0.47562 (21791) *********************** 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 346 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 307 time to evaluate : 1.687 Fit side-chains REVERT: A 62 LYS cc_start: 0.7328 (tttt) cc_final: 0.6364 (tppp) REVERT: A 139 LEU cc_start: 0.9059 (mm) cc_final: 0.8767 (mm) REVERT: A 197 GLU cc_start: 0.6057 (mt-10) cc_final: 0.5500 (mt-10) REVERT: B 62 LYS cc_start: 0.7541 (tttt) cc_final: 0.6811 (ttpt) REVERT: B 78 MET cc_start: 0.8750 (tpp) cc_final: 0.8375 (tpp) REVERT: B 117 ASP cc_start: 0.8208 (p0) cc_final: 0.7988 (p0) REVERT: B 175 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7180 (mt) REVERT: C 78 MET cc_start: 0.8844 (tpp) cc_final: 0.8482 (tpp) REVERT: C 171 TYR cc_start: 0.6810 (t80) cc_final: 0.6471 (t80) REVERT: C 197 GLU cc_start: 0.6066 (mt-10) cc_final: 0.5666 (tt0) REVERT: D 62 LYS cc_start: 0.7045 (tttt) cc_final: 0.6469 (tppt) REVERT: E 45 GLN cc_start: 0.8516 (pm20) cc_final: 0.8215 (pm20) REVERT: E 97 ASP cc_start: 0.7549 (m-30) cc_final: 0.7290 (m-30) REVERT: E 139 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8808 (mm) REVERT: F 45 GLN cc_start: 0.8353 (pm20) cc_final: 0.8140 (pm20) REVERT: G 37 GLN cc_start: 0.8474 (mt0) cc_final: 0.8143 (mm-40) REVERT: G 139 LEU cc_start: 0.8837 (mm) cc_final: 0.8457 (mm) REVERT: J 62 LYS cc_start: 0.6774 (tttt) cc_final: 0.6284 (tppt) REVERT: K 45 GLN cc_start: 0.8449 (pm20) cc_final: 0.8239 (pm20) REVERT: K 62 LYS cc_start: 0.7422 (tttt) cc_final: 0.6552 (tppp) outliers start: 39 outliers final: 26 residues processed: 329 average time/residue: 0.2360 time to fit residues: 121.0351 Evaluate side-chains 303 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 275 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 175 LEU 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 D residue 196 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 139 LEU 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 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 164 ASN Chi-restraints excluded: chain K residue 89 THR 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 151 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 145 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 134 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 30 GLN ** G 91 GLN ** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN K 30 GLN ** K 86 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.172410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128835 restraints weight = 19238.742| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.39 r_work: 0.3206 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16214 Z= 0.182 Angle : 0.529 12.127 21791 Z= 0.286 Chirality : 0.045 0.219 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.768 13.903 2255 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.14 % Allowed : 21.51 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2002 helix: 1.47 (0.18), residues: 781 sheet: 0.87 (0.25), residues: 484 loop : -0.34 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 84 HIS 0.005 0.001 HIS C 121 PHE 0.014 0.002 PHE F 110 TYR 0.025 0.002 TYR G 36 ARG 0.002 0.000 ARG G 156 Details of bonding type rmsd hydrogen bonds : bond 0.03801 ( 761) hydrogen bonds : angle 4.17758 ( 2250) covalent geometry : bond 0.00417 (16214) covalent geometry : angle 0.52906 (21791) *********************** 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 352 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 316 time to evaluate : 1.727 Fit side-chains REVERT: A 62 LYS cc_start: 0.7250 (tttt) cc_final: 0.6273 (tppp) REVERT: A 139 LEU cc_start: 0.9090 (mm) cc_final: 0.8832 (mm) REVERT: B 62 LYS cc_start: 0.7565 (tttt) cc_final: 0.6616 (tppp) REVERT: B 78 MET cc_start: 0.8784 (tpp) cc_final: 0.8455 (tpp) REVERT: C 78 MET cc_start: 0.8874 (tpp) cc_final: 0.8621 (tpp) REVERT: C 126 TYR cc_start: 0.8327 (t80) cc_final: 0.8050 (t80) REVERT: C 139 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 171 TYR cc_start: 0.6944 (t80) cc_final: 0.6697 (t80) REVERT: C 197 GLU cc_start: 0.6226 (mt-10) cc_final: 0.6011 (tt0) REVERT: D 62 LYS cc_start: 0.7019 (tttt) cc_final: 0.6391 (tppt) REVERT: E 97 ASP cc_start: 0.7574 (m-30) cc_final: 0.7338 (m-30) REVERT: E 139 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8807 (mm) REVERT: F 45 GLN cc_start: 0.8420 (pm20) cc_final: 0.8178 (pm20) REVERT: F 171 TYR cc_start: 0.7052 (t80) cc_final: 0.6762 (t80) REVERT: G 37 GLN cc_start: 0.8440 (mt0) cc_final: 0.8097 (mm-40) REVERT: G 139 LEU cc_start: 0.8921 (mm) cc_final: 0.8519 (mm) REVERT: I 62 LYS cc_start: 0.6886 (tttt) cc_final: 0.6482 (tppt) REVERT: J 62 LYS cc_start: 0.6675 (tttt) cc_final: 0.6218 (tppt) REVERT: K 45 GLN cc_start: 0.8512 (pm20) cc_final: 0.8288 (pm20) REVERT: K 62 LYS cc_start: 0.7380 (tttt) cc_final: 0.6701 (tppp) outliers start: 36 outliers final: 24 residues processed: 334 average time/residue: 0.2346 time to fit residues: 121.5267 Evaluate side-chains 298 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 1.943 ------------------------------------------------------------------------------- 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 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 139 LEU 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 E residue 139 LEU 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 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 123 ASP Chi-restraints excluded: chain K residue 89 THR 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 175 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 157 optimal weight: 0.7980 chunk 21 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 C 99 ASN C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 30 GLN ** 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 ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** 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 86 HIS ** 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 = 0.3911 r_free = 0.3911 target = 0.174372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.130825 restraints weight = 19103.588| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.46 r_work: 0.3252 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16214 Z= 0.111 Angle : 0.479 12.529 21791 Z= 0.257 Chirality : 0.043 0.164 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.556 13.235 2255 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.96 % Allowed : 22.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 2002 helix: 1.65 (0.18), residues: 781 sheet: 0.97 (0.25), residues: 484 loop : -0.29 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 84 HIS 0.003 0.001 HIS A 86 PHE 0.009 0.001 PHE B 110 TYR 0.033 0.001 TYR H 171 ARG 0.003 0.000 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.02900 ( 761) hydrogen bonds : angle 4.06810 ( 2250) covalent geometry : bond 0.00250 (16214) covalent geometry : angle 0.47868 (21791) *********************** 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 349 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 316 time to evaluate : 1.812 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9064 (mm) cc_final: 0.8788 (mm) REVERT: B 62 LYS cc_start: 0.7368 (tttt) cc_final: 0.6454 (tppp) REVERT: B 117 ASP cc_start: 0.8150 (p0) cc_final: 0.7938 (p0) REVERT: C 78 MET cc_start: 0.8774 (tpp) cc_final: 0.8436 (tpp) REVERT: C 126 TYR cc_start: 0.8447 (t80) cc_final: 0.8176 (t80) REVERT: C 139 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8646 (mm) REVERT: D 62 LYS cc_start: 0.6987 (tttt) cc_final: 0.6312 (tppt) REVERT: D 78 MET cc_start: 0.8623 (tpp) cc_final: 0.7888 (mmm) REVERT: E 97 ASP cc_start: 0.7581 (m-30) cc_final: 0.7318 (m-30) REVERT: E 139 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8796 (mm) REVERT: F 117 ASP cc_start: 0.8172 (p0) cc_final: 0.7727 (p0) REVERT: F 171 TYR cc_start: 0.6944 (t80) cc_final: 0.6666 (t80) REVERT: G 37 GLN cc_start: 0.8478 (mt0) cc_final: 0.8142 (mm-40) REVERT: G 62 LYS cc_start: 0.6639 (tttt) cc_final: 0.6049 (tppt) REVERT: G 139 LEU cc_start: 0.8840 (mm) cc_final: 0.8413 (mm) REVERT: H 62 LYS cc_start: 0.6961 (tttt) cc_final: 0.6237 (tppt) REVERT: I 62 LYS cc_start: 0.7035 (tttt) cc_final: 0.6587 (tppt) REVERT: J 62 LYS cc_start: 0.6494 (tttt) cc_final: 0.6058 (tppt) REVERT: K 62 LYS cc_start: 0.7246 (tttt) cc_final: 0.6610 (tppp) outliers start: 33 outliers final: 25 residues processed: 333 average time/residue: 0.2365 time to fit residues: 122.5390 Evaluate side-chains 312 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 285 time to evaluate : 1.747 ------------------------------------------------------------------------------- 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 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 164 ASN 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 E residue 139 LEU 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 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 123 ASP 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 176 optimal weight: 10.0000 chunk 110 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 149 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 76 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN K 121 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129705 restraints weight = 19159.792| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.41 r_work: 0.3263 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.3364 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= 0.152 Angle : 0.512 12.506 21791 Z= 0.277 Chirality : 0.044 0.166 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.659 16.173 2255 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.14 % Allowed : 21.87 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2002 helix: 1.57 (0.18), residues: 781 sheet: 0.91 (0.25), residues: 484 loop : -0.24 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 84 HIS 0.004 0.001 HIS A 86 PHE 0.012 0.001 PHE C 110 TYR 0.027 0.002 TYR H 171 ARG 0.002 0.000 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.03447 ( 761) hydrogen bonds : angle 4.12837 ( 2250) covalent geometry : bond 0.00347 (16214) covalent geometry : angle 0.51201 (21791) *********************** 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 343 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 307 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9091 (mm) cc_final: 0.8825 (mm) REVERT: B 62 LYS cc_start: 0.7315 (tttt) cc_final: 0.6467 (tppp) REVERT: B 117 ASP cc_start: 0.8123 (p0) cc_final: 0.7909 (p0) REVERT: C 78 MET cc_start: 0.8830 (tpp) cc_final: 0.8621 (tpp) REVERT: C 126 TYR cc_start: 0.8407 (t80) cc_final: 0.8152 (t80) REVERT: C 139 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8666 (mm) REVERT: D 62 LYS cc_start: 0.7033 (tttt) cc_final: 0.6359 (tppt) REVERT: E 97 ASP cc_start: 0.7609 (m-30) cc_final: 0.7382 (m-30) REVERT: E 139 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8813 (mm) REVERT: F 171 TYR cc_start: 0.7005 (t80) cc_final: 0.6761 (t80) REVERT: G 37 GLN cc_start: 0.8423 (mt0) cc_final: 0.7232 (mm-40) REVERT: G 62 LYS cc_start: 0.6692 (tttt) cc_final: 0.6127 (tppt) REVERT: G 139 LEU cc_start: 0.8914 (mm) cc_final: 0.8506 (mm) REVERT: H 62 LYS cc_start: 0.6948 (tttt) cc_final: 0.6417 (tppt) REVERT: I 139 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8738 (mm) REVERT: J 62 LYS cc_start: 0.6433 (tttt) cc_final: 0.5962 (tppt) REVERT: K 62 LYS cc_start: 0.7284 (tttt) cc_final: 0.6610 (tppp) outliers start: 36 outliers final: 29 residues processed: 326 average time/residue: 0.2265 time to fit residues: 115.1638 Evaluate side-chains 312 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 280 time to evaluate : 1.686 ------------------------------------------------------------------------------- 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 64 CYS 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 139 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 194 GLN 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 E residue 139 LEU 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 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain J residue 76 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 151 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN A 121 HIS B 30 GLN B 86 HIS ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 121 HIS C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 69 HIS ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN K 86 HIS ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.168799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.124686 restraints weight = 19409.201| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.40 r_work: 0.3204 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3704 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= 0.299 Angle : 0.645 12.919 21791 Z= 0.350 Chirality : 0.050 0.183 2299 Planarity : 0.004 0.023 2882 Dihedral : 4.250 19.291 2255 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.38 % Allowed : 21.69 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2002 helix: 1.14 (0.17), residues: 781 sheet: 0.37 (0.24), residues: 495 loop : -0.67 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 84 HIS 0.008 0.002 HIS C 121 PHE 0.017 0.002 PHE H 110 TYR 0.037 0.003 TYR H 171 ARG 0.003 0.000 ARG E 193 Details of bonding type rmsd hydrogen bonds : bond 0.04833 ( 761) hydrogen bonds : angle 4.41535 ( 2250) covalent geometry : bond 0.00684 (16214) covalent geometry : angle 0.64549 (21791) *********************** 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 317 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 1.741 Fit side-chains REVERT: A 139 LEU cc_start: 0.9107 (mm) cc_final: 0.8855 (mm) REVERT: B 62 LYS cc_start: 0.7349 (tttt) cc_final: 0.6487 (tppp) REVERT: B 139 LEU cc_start: 0.8814 (mm) cc_final: 0.8591 (mm) REVERT: C 78 MET cc_start: 0.8927 (tpp) cc_final: 0.8683 (tpp) REVERT: C 139 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8686 (mm) REVERT: C 171 TYR cc_start: 0.7009 (t80) cc_final: 0.6670 (t80) REVERT: E 97 ASP cc_start: 0.7736 (m-30) cc_final: 0.7499 (m-30) REVERT: E 139 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8830 (mm) REVERT: F 117 ASP cc_start: 0.8250 (p0) cc_final: 0.7882 (p0) REVERT: F 171 TYR cc_start: 0.7157 (t80) cc_final: 0.6921 (t80) REVERT: G 37 GLN cc_start: 0.8397 (mt0) cc_final: 0.8193 (mm-40) REVERT: G 62 LYS cc_start: 0.6774 (tttt) cc_final: 0.6329 (tppt) REVERT: G 139 LEU cc_start: 0.8961 (mm) cc_final: 0.8562 (mm) REVERT: H 62 LYS cc_start: 0.7066 (tttt) cc_final: 0.6529 (tppt) REVERT: I 139 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8751 (mm) REVERT: K 62 LYS cc_start: 0.7338 (tttt) cc_final: 0.6609 (tppp) outliers start: 40 outliers final: 32 residues processed: 300 average time/residue: 0.2312 time to fit residues: 107.9505 Evaluate side-chains 298 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 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 C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 139 LEU 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 139 LEU 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 G residue 89 THR 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 H residue 196 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 139 LEU 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 K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 108 CYS 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 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 82 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 76 ASN J 91 GLN J 164 ASN K 99 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.172401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.127983 restraints weight = 19376.949| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.50 r_work: 0.3227 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16214 Z= 0.129 Angle : 0.513 13.007 21791 Z= 0.279 Chirality : 0.045 0.167 2299 Planarity : 0.003 0.030 2882 Dihedral : 3.817 18.176 2255 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.02 % Allowed : 22.82 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.18), residues: 2002 helix: 1.56 (0.18), residues: 770 sheet: 0.81 (0.25), residues: 473 loop : -0.38 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 84 HIS 0.007 0.001 HIS K 86 PHE 0.010 0.001 PHE B 110 TYR 0.031 0.002 TYR H 171 ARG 0.002 0.000 ARG F 44 Details of bonding type rmsd hydrogen bonds : bond 0.03222 ( 761) hydrogen bonds : angle 4.15794 ( 2250) covalent geometry : bond 0.00289 (16214) covalent geometry : angle 0.51260 (21791) ********************** 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 339 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 1.798 Fit side-chains REVERT: A 139 LEU cc_start: 0.9090 (mm) cc_final: 0.8796 (mm) REVERT: B 62 LYS cc_start: 0.7311 (tttt) cc_final: 0.6460 (tppp) REVERT: B 97 ASP cc_start: 0.7648 (m-30) cc_final: 0.7411 (m-30) REVERT: C 78 MET cc_start: 0.8749 (tpp) cc_final: 0.8406 (tpp) REVERT: C 126 TYR cc_start: 0.8309 (t80) cc_final: 0.8103 (t80) REVERT: C 139 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8659 (mm) REVERT: E 97 ASP cc_start: 0.7658 (m-30) cc_final: 0.7390 (m-30) REVERT: E 139 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8795 (mm) REVERT: F 117 ASP cc_start: 0.8185 (p0) cc_final: 0.7745 (p0) REVERT: F 171 TYR cc_start: 0.6989 (t80) cc_final: 0.6733 (t80) REVERT: G 37 GLN cc_start: 0.8395 (mt0) cc_final: 0.8126 (mm-40) REVERT: G 62 LYS cc_start: 0.6841 (tttt) cc_final: 0.6245 (tppt) REVERT: G 78 MET cc_start: 0.8886 (tpp) cc_final: 0.8315 (mmm) REVERT: G 139 LEU cc_start: 0.8872 (mm) cc_final: 0.8429 (mm) REVERT: H 36 TYR cc_start: 0.8167 (t80) cc_final: 0.7875 (t80) REVERT: H 62 LYS cc_start: 0.6999 (tttt) cc_final: 0.6452 (tppt) REVERT: I 139 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8699 (mm) REVERT: K 62 LYS cc_start: 0.7108 (tttt) cc_final: 0.6393 (tppp) outliers start: 34 outliers final: 23 residues processed: 326 average time/residue: 0.2225 time to fit residues: 114.5616 Evaluate side-chains 305 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 279 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR 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 C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 139 LEU 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 E residue 139 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 89 THR 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 H residue 196 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain J residue 43 LEU 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 69 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 8 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 128 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.169035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124989 restraints weight = 19449.261| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.42 r_work: 0.3199 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16214 Z= 0.240 Angle : 0.602 12.656 21791 Z= 0.328 Chirality : 0.048 0.179 2299 Planarity : 0.004 0.031 2882 Dihedral : 4.095 20.246 2255 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.02 % Allowed : 23.11 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.18), residues: 2002 helix: 1.24 (0.18), residues: 781 sheet: 0.28 (0.24), residues: 506 loop : -0.52 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 84 HIS 0.010 0.002 HIS K 86 PHE 0.016 0.002 PHE I 110 TYR 0.033 0.002 TYR H 171 ARG 0.002 0.000 ARG K 204 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 761) hydrogen bonds : angle 4.30567 ( 2250) covalent geometry : bond 0.00552 (16214) covalent geometry : angle 0.60178 (21791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6925.32 seconds wall clock time: 121 minutes 8.50 seconds (7268.50 seconds total)