Starting phenix.real_space_refine on Fri Jun 13 23:48:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h1p_34430/06_2025/8h1p_34430.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h1p_34430/06_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_34430/06_2025/8h1p_34430.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h1p_34430/06_2025/8h1p_34430.map" model { file = "/net/cci-nas-00/data/ceres_data/8h1p_34430/06_2025/8h1p_34430.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h1p_34430/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 5.07, per 1000 atoms: 0.32 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: 4.07 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: 1.70 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: 5.58 Time building geometry restraints manager: 4.88 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: 0.640 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: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 35.010 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.110 ------------------------------------------------------------------------------- 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 : 1.898 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: 0.2650 time to fit residues: 165.3559 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 : 1.942 ------------------------------------------------------------------------------- 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 = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.131450 restraints weight = 19394.563| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.48 r_work: 0.3296 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 1.691 Fit side-chains revert: symmetry clash REVERT: A 52 ILE cc_start: 0.7520 (mp) cc_final: 0.7192 (mp) REVERT: A 62 LYS cc_start: 0.7407 (tttt) cc_final: 0.6366 (tppp) REVERT: A 139 LEU cc_start: 0.9018 (mm) cc_final: 0.8784 (mm) REVERT: A 195 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7568 (t0) REVERT: B 62 LYS cc_start: 0.7205 (tttt) cc_final: 0.6469 (ttpt) REVERT: B 117 ASP cc_start: 0.8272 (p0) cc_final: 0.7995 (p0) REVERT: B 195 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7647 (t0) REVERT: C 126 TYR cc_start: 0.8328 (t80) cc_final: 0.8080 (t80) REVERT: C 195 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7898 (t0) REVERT: D 139 LEU cc_start: 0.8900 (mm) cc_final: 0.8694 (mm) REVERT: E 149 ASP cc_start: 0.8383 (m-30) cc_final: 0.8180 (m-30) REVERT: F 97 ASP cc_start: 0.7311 (m-30) cc_final: 0.7095 (m-30) REVERT: F 139 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8694 (mm) REVERT: F 195 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7490 (t0) REVERT: G 37 GLN cc_start: 0.8491 (mt0) cc_final: 0.8150 (mm-40) REVERT: H 91 GLN cc_start: 0.8438 (tt0) cc_final: 0.8220 (tt0) REVERT: H 126 TYR cc_start: 0.8347 (t80) cc_final: 0.8114 (t80) REVERT: H 195 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7471 (t0) REVERT: I 77 GLU cc_start: 0.7029 (pt0) cc_final: 0.6693 (pt0) REVERT: I 195 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7715 (t0) REVERT: J 62 LYS cc_start: 0.6917 (tttt) cc_final: 0.6330 (tppt) REVERT: J 195 ASP cc_start: 0.8092 (OUTLIER) cc_final: 0.7660 (t0) REVERT: K 62 LYS cc_start: 0.7298 (tttt) cc_final: 0.6504 (tppp) REVERT: K 78 MET cc_start: 0.8912 (tpp) cc_final: 0.8669 (tpp) REVERT: K 195 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7899 (t0) outliers start: 50 outliers final: 16 residues processed: 389 average time/residue: 0.2485 time to fit residues: 147.8584 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 : 1.789 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 197 optimal weight: 0.0060 chunk 54 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 overall best weight: 0.8198 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.178151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133252 restraints weight = 19137.842| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.48 r_work: 0.3270 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16214 Z= 0.110 Angle : 0.464 8.010 21791 Z= 0.252 Chirality : 0.043 0.214 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.528 15.500 2255 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.67 % Allowed : 19.31 % Favored : 78.02 % 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: 1.16 (0.18), residues: 2002 helix: 1.45 (0.18), residues: 781 sheet: 1.14 (0.26), residues: 473 loop : -0.10 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 84 HIS 0.003 0.001 HIS A 86 PHE 0.008 0.001 PHE J 110 TYR 0.017 0.001 TYR G 36 ARG 0.002 0.000 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.03034 ( 761) hydrogen bonds : angle 4.09404 ( 2250) covalent geometry : bond 0.00250 (16214) covalent geometry : angle 0.46426 (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 411 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 1.893 Fit side-chains revert: symmetry clash REVERT: A 195 ASP cc_start: 0.7865 (OUTLIER) cc_final: 0.7615 (t0) REVERT: B 45 GLN cc_start: 0.8269 (pm20) cc_final: 0.7985 (pm20) REVERT: B 62 LYS cc_start: 0.7326 (tttt) cc_final: 0.6606 (ttpt) REVERT: B 78 MET cc_start: 0.8713 (tpp) cc_final: 0.8507 (tpp) REVERT: B 117 ASP cc_start: 0.8249 (p0) cc_final: 0.8019 (p0) REVERT: B 139 LEU cc_start: 0.8884 (mm) cc_final: 0.8584 (mm) REVERT: B 195 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7501 (t0) REVERT: C 45 GLN cc_start: 0.8432 (pm20) cc_final: 0.8131 (pm20) REVERT: C 78 MET cc_start: 0.8887 (tpp) cc_final: 0.8399 (tpp) REVERT: C 126 TYR cc_start: 0.8311 (t80) cc_final: 0.7980 (t80) REVERT: C 195 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7648 (t0) REVERT: D 55 ARG cc_start: 0.6700 (mtp180) cc_final: 0.6489 (mtm180) REVERT: D 64 CYS cc_start: 0.8580 (t) cc_final: 0.8328 (t) REVERT: E 139 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8794 (mm) REVERT: F 97 ASP cc_start: 0.7379 (m-30) cc_final: 0.7154 (m-30) REVERT: F 139 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8708 (mm) REVERT: G 37 GLN cc_start: 0.8446 (mt0) cc_final: 0.8108 (mm-40) REVERT: G 145 GLU cc_start: 0.7935 (tt0) cc_final: 0.7726 (tt0) REVERT: H 126 TYR cc_start: 0.8382 (t80) cc_final: 0.8120 (t80) REVERT: H 145 GLU cc_start: 0.8033 (tt0) cc_final: 0.7770 (tt0) REVERT: I 195 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7897 (t0) REVERT: J 62 LYS cc_start: 0.6800 (tttt) cc_final: 0.6262 (tppt) REVERT: K 45 GLN cc_start: 0.8368 (pm20) cc_final: 0.7538 (pm20) REVERT: K 62 LYS cc_start: 0.7378 (tttt) cc_final: 0.6582 (tppp) REVERT: K 78 MET cc_start: 0.8879 (tpp) cc_final: 0.8602 (tpp) REVERT: K 139 LEU cc_start: 0.9053 (mm) cc_final: 0.8837 (mm) REVERT: K 195 ASP cc_start: 0.8162 (OUTLIER) cc_final: 0.7946 (t0) outliers start: 45 outliers final: 23 residues processed: 392 average time/residue: 0.2476 time to fit residues: 149.4558 Evaluate side-chains 318 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 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 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain 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 Chi-restraints excluded: chain K residue 195 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 124 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 139 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 82 optimal weight: 0.0970 chunk 3 optimal weight: 8.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN 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 ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN J 99 ASN K 30 GLN ** K 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.176475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131879 restraints weight = 18980.853| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.43 r_work: 0.3273 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16214 Z= 0.107 Angle : 0.459 12.381 21791 Z= 0.248 Chirality : 0.042 0.142 2299 Planarity : 0.002 0.021 2882 Dihedral : 3.444 15.140 2255 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.79 % Allowed : 20.02 % Favored : 77.18 % 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: 1.27 (0.19), residues: 2002 helix: 1.67 (0.18), residues: 781 sheet: 1.09 (0.25), residues: 484 loop : -0.15 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 84 HIS 0.003 0.001 HIS A 86 PHE 0.009 0.001 PHE J 110 TYR 0.016 0.001 TYR G 36 ARG 0.002 0.000 ARG J 44 Details of bonding type rmsd hydrogen bonds : bond 0.02914 ( 761) hydrogen bonds : angle 4.05534 ( 2250) covalent geometry : bond 0.00241 (16214) covalent geometry : angle 0.45876 (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 365 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 318 time to evaluate : 1.603 Fit side-chains revert: symmetry clash REVERT: A 195 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.7536 (t0) REVERT: B 62 LYS cc_start: 0.7516 (tttt) cc_final: 0.6796 (ttpt) REVERT: B 117 ASP cc_start: 0.8263 (p0) cc_final: 0.8063 (p0) REVERT: C 78 MET cc_start: 0.8825 (tpp) cc_final: 0.8426 (tpp) REVERT: C 126 TYR cc_start: 0.8311 (t80) cc_final: 0.8014 (t80) REVERT: C 139 LEU cc_start: 0.8930 (mm) cc_final: 0.8712 (mm) REVERT: D 45 GLN cc_start: 0.8513 (pm20) cc_final: 0.8270 (pm20) REVERT: D 62 LYS cc_start: 0.7147 (tttt) cc_final: 0.6524 (tppt) REVERT: E 45 GLN cc_start: 0.8469 (pm20) cc_final: 0.8234 (pm20) REVERT: E 139 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8788 (mm) REVERT: E 149 ASP cc_start: 0.8375 (m-30) cc_final: 0.8172 (m-30) REVERT: F 97 ASP cc_start: 0.7365 (m-30) cc_final: 0.7153 (m-30) REVERT: G 37 GLN cc_start: 0.8503 (mt0) cc_final: 0.8166 (mm-40) REVERT: G 126 TYR cc_start: 0.8278 (t80) cc_final: 0.8004 (t80) REVERT: G 139 LEU cc_start: 0.8773 (mm) cc_final: 0.8406 (mm) REVERT: H 145 GLU cc_start: 0.7981 (tt0) cc_final: 0.7727 (tt0) REVERT: J 62 LYS cc_start: 0.6828 (tttt) cc_final: 0.6300 (tppt) REVERT: K 62 LYS cc_start: 0.7329 (tttt) cc_final: 0.6524 (tppp) outliers start: 47 outliers final: 26 residues processed: 348 average time/residue: 0.2314 time to fit residues: 126.8819 Evaluate side-chains 325 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 297 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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 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 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 F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 166 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 124 optimal weight: 8.9990 chunk 197 optimal weight: 0.0770 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 overall best weight: 2.3944 ------------------------------------------------------------------------------- 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 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** C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 121 HIS ** 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 ** 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 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 164 ASN K 30 GLN K 86 HIS K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.172169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127393 restraints weight = 19387.212| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.41 r_work: 0.3209 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16214 Z= 0.189 Angle : 0.534 12.091 21791 Z= 0.287 Chirality : 0.046 0.258 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.728 14.624 2255 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.44 % Allowed : 20.74 % Favored : 76.83 % 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: 1.04 (0.18), residues: 2002 helix: 1.55 (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 0.009 0.002 TRP B 84 HIS 0.005 0.001 HIS K 86 PHE 0.015 0.002 PHE A 110 TYR 0.023 0.002 TYR G 36 ARG 0.002 0.000 ARG G 143 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 761) hydrogen bonds : angle 4.15185 ( 2250) covalent geometry : bond 0.00432 (16214) covalent geometry : angle 0.53366 (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 349 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 308 time to evaluate : 1.700 Fit side-chains REVERT: A 195 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7730 (t0) REVERT: B 62 LYS cc_start: 0.7554 (tttt) cc_final: 0.6826 (ttpt) REVERT: B 117 ASP cc_start: 0.8265 (p0) cc_final: 0.8004 (p0) REVERT: B 175 LEU cc_start: 0.7351 (OUTLIER) cc_final: 0.7143 (mt) REVERT: C 78 MET cc_start: 0.8865 (tpp) cc_final: 0.8580 (tpp) REVERT: C 126 TYR cc_start: 0.8308 (t80) cc_final: 0.7982 (t80) REVERT: C 139 LEU cc_start: 0.8952 (mm) cc_final: 0.8750 (mm) REVERT: C 171 TYR cc_start: 0.6867 (t80) cc_final: 0.6552 (t80) REVERT: D 45 GLN cc_start: 0.8532 (pm20) cc_final: 0.8242 (pm20) REVERT: D 62 LYS cc_start: 0.6989 (tttt) cc_final: 0.6444 (tppt) REVERT: E 45 GLN cc_start: 0.8553 (pm20) cc_final: 0.8264 (pm20) REVERT: E 97 ASP cc_start: 0.7622 (m-30) cc_final: 0.7381 (m-30) REVERT: E 139 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8801 (mm) REVERT: E 149 ASP cc_start: 0.8511 (m-30) cc_final: 0.8277 (m-30) REVERT: G 37 GLN cc_start: 0.8475 (mt0) cc_final: 0.8137 (mm-40) REVERT: G 139 LEU cc_start: 0.8916 (mm) cc_final: 0.8550 (mm) REVERT: J 62 LYS cc_start: 0.6845 (tttt) cc_final: 0.6313 (tppt) REVERT: K 62 LYS cc_start: 0.7396 (tttt) cc_final: 0.6531 (tppp) outliers start: 41 outliers final: 26 residues processed: 329 average time/residue: 0.2256 time to fit residues: 116.9173 Evaluate side-chains 304 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 166 ILE 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 64 CYS 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 90 GLN Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 151 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 76 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 ** 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 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN K 99 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.175487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.131407 restraints weight = 19094.482| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 2.41 r_work: 0.3260 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2903 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= 0.106 Angle : 0.460 12.325 21791 Z= 0.249 Chirality : 0.043 0.201 2299 Planarity : 0.002 0.021 2882 Dihedral : 3.523 13.287 2255 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.08 % Allowed : 21.39 % 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: 1.25 (0.19), residues: 2002 helix: 1.72 (0.18), residues: 781 sheet: 1.01 (0.25), residues: 484 loop : -0.19 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 84 HIS 0.003 0.001 HIS A 86 PHE 0.009 0.001 PHE B 110 TYR 0.021 0.001 TYR D 171 ARG 0.002 0.000 ARG F 143 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 761) hydrogen bonds : angle 4.00167 ( 2250) covalent geometry : bond 0.00236 (16214) covalent geometry : angle 0.45997 (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 358 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 323 time to evaluate : 1.694 Fit side-chains REVERT: A 62 LYS cc_start: 0.7430 (tttt) cc_final: 0.6501 (tppp) REVERT: A 139 LEU cc_start: 0.9063 (mm) cc_final: 0.8776 (mm) REVERT: B 62 LYS cc_start: 0.7539 (tttt) cc_final: 0.6818 (ttpt) REVERT: B 117 ASP cc_start: 0.8212 (p0) cc_final: 0.7939 (p0) REVERT: C 78 MET cc_start: 0.8853 (tpp) cc_final: 0.8476 (tpp) REVERT: C 126 TYR cc_start: 0.8391 (t80) cc_final: 0.8118 (t80) REVERT: C 139 LEU cc_start: 0.8930 (mm) cc_final: 0.8719 (mm) REVERT: C 171 TYR cc_start: 0.6853 (t80) cc_final: 0.6568 (t80) REVERT: D 62 LYS cc_start: 0.7061 (tttt) cc_final: 0.6473 (tppt) REVERT: E 97 ASP cc_start: 0.7541 (m-30) cc_final: 0.7285 (m-30) REVERT: E 139 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8795 (mm) REVERT: G 37 GLN cc_start: 0.8453 (mt0) cc_final: 0.8143 (mm-40) REVERT: G 91 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: G 139 LEU cc_start: 0.8899 (mm) cc_final: 0.8505 (mm) REVERT: J 62 LYS cc_start: 0.6738 (tttt) cc_final: 0.6222 (tppt) REVERT: K 62 LYS cc_start: 0.7162 (tttt) cc_final: 0.6568 (tppp) outliers start: 35 outliers final: 24 residues processed: 340 average time/residue: 0.2255 time to fit residues: 120.3578 Evaluate side-chains 312 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 286 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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 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 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 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 166 ILE 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: 3.9990 chunk 186 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 192 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 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 ** 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 30 GLN J 76 ASN ** 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** J 164 ASN K 30 GLN ** 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 = 0.3895 r_free = 0.3895 target = 0.172972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128970 restraints weight = 19105.085| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.37 r_work: 0.3225 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16214 Z= 0.161 Angle : 0.515 12.311 21791 Z= 0.280 Chirality : 0.045 0.193 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.664 17.891 2255 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.14 % Allowed : 21.69 % Favored : 76.17 % 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: 1.11 (0.19), residues: 2002 helix: 1.61 (0.18), residues: 781 sheet: 0.92 (0.25), residues: 484 loop : -0.28 (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 C 121 PHE 0.012 0.001 PHE I 110 TYR 0.022 0.002 TYR G 36 ARG 0.001 0.000 ARG E 44 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 761) hydrogen bonds : angle 4.14069 ( 2250) covalent geometry : bond 0.00367 (16214) covalent geometry : angle 0.51496 (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 333 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 2.497 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9086 (mm) cc_final: 0.8815 (mm) REVERT: B 62 LYS cc_start: 0.7507 (tttt) cc_final: 0.6577 (tppp) REVERT: B 117 ASP cc_start: 0.8263 (p0) cc_final: 0.8005 (p0) REVERT: B 195 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: C 78 MET cc_start: 0.8882 (tpp) cc_final: 0.8574 (tpp) REVERT: C 126 TYR cc_start: 0.8336 (t80) cc_final: 0.8061 (t80) REVERT: C 139 LEU cc_start: 0.8990 (mm) cc_final: 0.8762 (mm) REVERT: D 62 LYS cc_start: 0.7045 (tttt) cc_final: 0.6361 (tppt) REVERT: D 78 MET cc_start: 0.8717 (tpp) cc_final: 0.8381 (mmm) REVERT: E 97 ASP cc_start: 0.7611 (m-30) cc_final: 0.7364 (m-30) REVERT: E 139 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8789 (mm) REVERT: E 196 LEU cc_start: 0.7939 (tp) cc_final: 0.7642 (mp) REVERT: F 171 TYR cc_start: 0.6930 (t80) cc_final: 0.6664 (t80) REVERT: G 37 GLN cc_start: 0.8456 (mt0) cc_final: 0.8122 (mm-40) REVERT: G 91 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: G 139 LEU cc_start: 0.8920 (mm) cc_final: 0.8529 (mm) REVERT: H 97 ASP cc_start: 0.7331 (m-30) cc_final: 0.7128 (m-30) REVERT: I 62 LYS cc_start: 0.6922 (tttt) cc_final: 0.6522 (tppt) REVERT: I 139 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8813 (mm) REVERT: J 62 LYS cc_start: 0.6590 (tttt) cc_final: 0.6192 (tppt) REVERT: K 62 LYS cc_start: 0.7333 (tttt) cc_final: 0.6710 (tppp) outliers start: 36 outliers final: 25 residues processed: 316 average time/residue: 0.3045 time to fit residues: 149.1276 Evaluate side-chains 298 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 269 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 B residue 195 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 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 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain J residue 76 ASN 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 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 176 optimal weight: 3.9990 chunk 110 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 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 ** 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 G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 HIS ** 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** J 164 ASN K 30 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.172450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.128528 restraints weight = 19120.331| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.40 r_work: 0.3226 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16214 Z= 0.159 Angle : 0.516 12.813 21791 Z= 0.281 Chirality : 0.045 0.174 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.724 18.261 2255 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.08 % Allowed : 21.33 % Favored : 76.59 % 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: 1.06 (0.19), residues: 2002 helix: 1.56 (0.18), residues: 781 sheet: 0.90 (0.25), residues: 484 loop : -0.28 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 84 HIS 0.004 0.001 HIS C 121 PHE 0.013 0.001 PHE B 110 TYR 0.034 0.002 TYR C 171 ARG 0.001 0.000 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 761) hydrogen bonds : angle 4.14304 ( 2250) covalent geometry : bond 0.00363 (16214) covalent geometry : angle 0.51588 (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 340 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 1.844 Fit side-chains REVERT: A 139 LEU cc_start: 0.9095 (mm) cc_final: 0.8830 (mm) REVERT: B 62 LYS cc_start: 0.7306 (tttt) cc_final: 0.6454 (tppp) REVERT: C 78 MET cc_start: 0.8897 (tpp) cc_final: 0.8632 (tpp) REVERT: C 126 TYR cc_start: 0.8384 (t80) cc_final: 0.8121 (t80) REVERT: C 139 LEU cc_start: 0.8996 (mm) cc_final: 0.8761 (mm) REVERT: D 62 LYS cc_start: 0.7039 (tttt) cc_final: 0.6361 (tppt) REVERT: D 171 TYR cc_start: 0.6766 (t80) cc_final: 0.6565 (t80) REVERT: E 97 ASP cc_start: 0.7597 (m-30) cc_final: 0.7363 (m-30) REVERT: E 139 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8799 (mm) REVERT: E 196 LEU cc_start: 0.8032 (tp) cc_final: 0.7827 (mp) REVERT: F 171 TYR cc_start: 0.7005 (t80) cc_final: 0.6663 (t80) REVERT: G 37 GLN cc_start: 0.8464 (mt0) cc_final: 0.7307 (mm-40) REVERT: G 62 LYS cc_start: 0.6656 (tttt) cc_final: 0.6101 (tppt) REVERT: G 91 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8013 (tt0) REVERT: G 139 LEU cc_start: 0.8932 (mm) cc_final: 0.8536 (mm) REVERT: H 45 GLN cc_start: 0.8573 (pm20) cc_final: 0.8260 (pm20) REVERT: H 62 LYS cc_start: 0.7018 (tttt) cc_final: 0.6436 (tppt) REVERT: I 139 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8772 (mm) REVERT: J 62 LYS cc_start: 0.6491 (tttt) cc_final: 0.6041 (tppt) REVERT: K 62 LYS cc_start: 0.7308 (tttt) cc_final: 0.6610 (tppp) outliers start: 35 outliers final: 24 residues processed: 323 average time/residue: 0.2423 time to fit residues: 121.7932 Evaluate side-chains 295 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 268 time to evaluate : 1.767 ------------------------------------------------------------------------------- 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 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 G residue 89 THR Chi-restraints excluded: chain G residue 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain 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 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 180 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 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 ** 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** G 99 ASN H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN I 69 HIS ** 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 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** J 164 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.171650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.127357 restraints weight = 19198.495| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.42 r_work: 0.3238 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16214 Z= 0.190 Angle : 0.551 13.102 21791 Z= 0.300 Chirality : 0.046 0.193 2299 Planarity : 0.003 0.026 2882 Dihedral : 3.863 18.724 2255 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.72 % Allowed : 21.39 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2002 helix: 1.50 (0.18), residues: 770 sheet: 0.80 (0.25), residues: 484 loop : -0.40 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 84 HIS 0.005 0.001 HIS C 121 PHE 0.014 0.002 PHE I 110 TYR 0.030 0.002 TYR A 171 ARG 0.002 0.000 ARG F 204 Details of bonding type rmsd hydrogen bonds : bond 0.03879 ( 761) hydrogen bonds : angle 4.21429 ( 2250) covalent geometry : bond 0.00436 (16214) covalent geometry : angle 0.55104 (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 318 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 289 time to evaluate : 1.874 Fit side-chains REVERT: A 139 LEU cc_start: 0.9095 (mm) cc_final: 0.8819 (mm) REVERT: B 62 LYS cc_start: 0.7323 (tttt) cc_final: 0.6480 (tppp) REVERT: B 117 ASP cc_start: 0.8157 (p0) cc_final: 0.7901 (p0) REVERT: B 173 ARG cc_start: 0.7665 (ttp-110) cc_final: 0.7364 (ttp-170) REVERT: C 78 MET cc_start: 0.8900 (tpp) cc_final: 0.8636 (tpp) REVERT: C 126 TYR cc_start: 0.8349 (t80) cc_final: 0.8105 (t80) REVERT: C 139 LEU cc_start: 0.9010 (mm) cc_final: 0.8782 (mm) REVERT: D 37 GLN cc_start: 0.8361 (mt0) cc_final: 0.7921 (mm-40) REVERT: D 62 LYS cc_start: 0.7036 (tttt) cc_final: 0.6357 (tppt) REVERT: E 62 LYS cc_start: 0.6873 (tttt) cc_final: 0.6356 (tppt) REVERT: E 97 ASP cc_start: 0.7633 (m-30) cc_final: 0.7407 (m-30) REVERT: E 139 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8817 (mm) REVERT: E 196 LEU cc_start: 0.8151 (tp) cc_final: 0.7921 (mp) REVERT: F 117 ASP cc_start: 0.8158 (p0) cc_final: 0.7800 (p0) REVERT: F 171 TYR cc_start: 0.7000 (t80) cc_final: 0.6702 (t80) REVERT: G 37 GLN cc_start: 0.8446 (mt0) cc_final: 0.8215 (mm-40) REVERT: G 62 LYS cc_start: 0.6645 (tttt) cc_final: 0.6111 (tppt) REVERT: G 91 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: G 139 LEU cc_start: 0.8946 (mm) cc_final: 0.8552 (mm) REVERT: H 45 GLN cc_start: 0.8578 (pm20) cc_final: 0.8242 (pm20) REVERT: H 62 LYS cc_start: 0.7058 (tttt) cc_final: 0.6517 (tppt) REVERT: I 139 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8769 (mm) REVERT: J 62 LYS cc_start: 0.6545 (tttt) cc_final: 0.6056 (tppt) REVERT: K 62 LYS cc_start: 0.7301 (tttt) cc_final: 0.6573 (tppp) outliers start: 29 outliers final: 23 residues processed: 306 average time/residue: 0.2478 time to fit residues: 117.3728 Evaluate side-chains 293 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 267 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 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 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 133 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 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 ** 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 G 99 ASN H 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 69 HIS ** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.170923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126919 restraints weight = 19367.366| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.41 r_work: 0.3251 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16214 Z= 0.198 Angle : 0.560 13.417 21791 Z= 0.306 Chirality : 0.047 0.185 2299 Planarity : 0.003 0.034 2882 Dihedral : 3.931 18.664 2255 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.66 % Allowed : 21.75 % Favored : 76.59 % 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: 0.81 (0.18), residues: 2002 helix: 1.46 (0.18), residues: 770 sheet: 0.69 (0.25), residues: 484 loop : -0.46 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 84 HIS 0.005 0.001 HIS C 121 PHE 0.014 0.002 PHE I 110 TYR 0.028 0.002 TYR C 171 ARG 0.002 0.000 ARG D 204 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 761) hydrogen bonds : angle 4.21375 ( 2250) covalent geometry : bond 0.00454 (16214) covalent geometry : angle 0.56023 (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 305 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 277 time to evaluate : 1.682 Fit side-chains REVERT: A 139 LEU cc_start: 0.9118 (mm) cc_final: 0.8845 (mm) REVERT: B 62 LYS cc_start: 0.7336 (tttt) cc_final: 0.6471 (tppp) REVERT: B 117 ASP cc_start: 0.8159 (p0) cc_final: 0.7911 (p0) REVERT: B 195 ASP cc_start: 0.8025 (m-30) cc_final: 0.7803 (m-30) REVERT: C 78 MET cc_start: 0.8871 (tpp) cc_final: 0.8632 (tpp) REVERT: C 126 TYR cc_start: 0.8352 (t80) cc_final: 0.8095 (t80) REVERT: C 139 LEU cc_start: 0.8994 (mm) cc_final: 0.8751 (mm) REVERT: D 37 GLN cc_start: 0.8364 (mt0) cc_final: 0.7913 (mm-40) REVERT: E 97 ASP cc_start: 0.7682 (m-30) cc_final: 0.7450 (m-30) REVERT: E 139 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8815 (mm) REVERT: E 196 LEU cc_start: 0.8150 (tp) cc_final: 0.7942 (mp) REVERT: F 117 ASP cc_start: 0.8192 (p0) cc_final: 0.7829 (p0) REVERT: F 171 TYR cc_start: 0.7032 (t80) cc_final: 0.6808 (t80) REVERT: G 37 GLN cc_start: 0.8433 (mt0) cc_final: 0.8146 (mm-40) REVERT: G 62 LYS cc_start: 0.6901 (tttt) cc_final: 0.6331 (tppt) REVERT: G 91 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8082 (tt0) REVERT: G 139 LEU cc_start: 0.8950 (mm) cc_final: 0.8539 (mm) REVERT: H 45 GLN cc_start: 0.8547 (pm20) cc_final: 0.8216 (pm20) REVERT: H 62 LYS cc_start: 0.7031 (tttt) cc_final: 0.6508 (tppt) REVERT: I 139 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8762 (mm) REVERT: K 62 LYS cc_start: 0.7238 (tttt) cc_final: 0.6475 (tppp) outliers start: 28 outliers final: 23 residues processed: 292 average time/residue: 0.2263 time to fit residues: 104.1703 Evaluate side-chains 292 residues out of total 1683 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 266 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 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 91 GLN Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 69 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 192 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- 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 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 ** 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 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 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 = 0.3903 r_free = 0.3903 target = 0.173173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.129401 restraints weight = 19304.450| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.43 r_work: 0.3250 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16214 Z= 0.151 Angle : 0.527 13.467 21791 Z= 0.288 Chirality : 0.045 0.166 2299 Planarity : 0.003 0.035 2882 Dihedral : 3.837 19.298 2255 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.66 % Allowed : 21.98 % 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: 0.84 (0.19), residues: 2002 helix: 1.49 (0.18), residues: 781 sheet: 0.49 (0.24), residues: 506 loop : -0.32 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 84 HIS 0.003 0.001 HIS E 121 PHE 0.012 0.001 PHE B 110 TYR 0.027 0.002 TYR C 171 ARG 0.003 0.000 ARG C 204 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 761) hydrogen bonds : angle 4.15301 ( 2250) covalent geometry : bond 0.00346 (16214) covalent geometry : angle 0.52738 (21791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7062.49 seconds wall clock time: 123 minutes 58.54 seconds (7438.54 seconds total)