Starting phenix.real_space_refine on Fri Sep 27 09:19:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/09_2024/8h1p_34430.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/09_2024/8h1p_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/09_2024/8h1p_34430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/09_2024/8h1p_34430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/09_2024/8h1p_34430.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/09_2024/8h1p_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-5461/modules/chem_data/mon_lib" Total number of atoms: 15950 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Restraints were copied for chains: C, B, E, D, G, F, I, H, K, J Time building chain proxies: 4.45, per 1000 atoms: 0.28 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: 3.58 Conformation dependent library (CDL) restraints added in 1.9 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: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER A 157 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE A 166 " --> pdb=" O GLY A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 177 Processing helix chain 'A' and resid 197 through 207 Processing helix chain 'B' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN B 45 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 79 Processing helix chain 'B' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE B 166 " --> pdb=" O GLY B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 197 through 207 Processing helix chain 'C' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN C 45 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 79 Processing helix chain 'C' and resid 134 through 157 removed outlier: 4.032A pdb=" N SER C 157 " --> pdb=" O ARG C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE C 166 " --> pdb=" O GLY C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 177 Processing helix chain 'C' and resid 197 through 207 Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 79 Processing helix chain 'D' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE D 166 " --> pdb=" O GLY D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 197 through 207 Processing helix chain 'E' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN E 45 " --> pdb=" O LYS E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 79 Processing helix chain 'E' and resid 134 through 157 removed outlier: 4.030A pdb=" N SER E 157 " --> pdb=" O ARG E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE E 166 " --> pdb=" O GLY E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 177 Processing helix chain 'E' and resid 197 through 207 Processing helix chain 'F' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN F 45 " --> pdb=" O LYS F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 79 Processing helix chain 'F' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE F 166 " --> pdb=" O GLY F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 177 Processing helix chain 'F' and resid 197 through 208 Processing helix chain 'G' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 79 Processing helix chain 'G' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER G 157 " --> pdb=" O ARG G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE G 166 " --> pdb=" O GLY G 163 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 177 Processing helix chain 'G' and resid 197 through 207 Processing helix chain 'H' and resid 32 through 45 removed outlier: 3.880A pdb=" N GLN H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 79 Processing helix chain 'H' and resid 134 through 157 removed outlier: 4.032A pdb=" N SER H 157 " --> pdb=" O ARG H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE H 166 " --> pdb=" O GLY H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 177 Processing helix chain 'H' and resid 197 through 207 Processing helix chain 'I' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN I 45 " --> pdb=" O LYS I 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 Processing helix chain 'I' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE I 166 " --> pdb=" O GLY I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 177 Processing helix chain 'I' and resid 197 through 207 Processing helix chain 'J' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN J 45 " --> pdb=" O LYS J 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 79 Processing helix chain 'J' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER J 157 " --> pdb=" O ARG J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 163 through 167 removed outlier: 3.511A pdb=" N ILE J 166 " --> pdb=" O GLY J 163 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 177 Processing helix chain 'J' and resid 197 through 207 Processing helix chain 'K' and resid 32 through 45 removed outlier: 3.881A pdb=" N GLN K 45 " --> pdb=" O LYS K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 79 Processing helix chain 'K' and resid 134 through 157 removed outlier: 4.031A pdb=" N SER K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 167 removed outlier: 3.510A pdb=" N ILE K 166 " --> pdb=" O GLY K 163 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 177 Processing helix chain 'K' and resid 197 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 99 removed outlier: 5.377A pdb=" N HIS A 86 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN A 114 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE A 88 " --> pdb=" O ARG A 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 112 " --> pdb=" O ILE A 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 90 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 106 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 96 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR A 104 " --> pdb=" O VAL A 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 98 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 52 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS B 86 " --> pdb=" O GLN B 114 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLN B 114 " --> pdb=" O HIS B 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE B 88 " --> pdb=" O ARG B 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG B 112 " --> pdb=" O ILE B 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN B 90 " --> pdb=" O PHE B 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY B 106 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL B 96 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR B 104 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 98 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS B 102 " --> pdb=" O LEU B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS C 86 " --> pdb=" O GLN C 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN C 114 " --> pdb=" O HIS C 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE C 88 " --> pdb=" O ARG C 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG C 112 " --> pdb=" O ILE C 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN C 90 " --> pdb=" O PHE C 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY C 106 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL C 96 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR C 104 " --> pdb=" O VAL C 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU C 98 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 52 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS D 86 " --> pdb=" O GLN D 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN D 114 " --> pdb=" O HIS D 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE D 88 " --> pdb=" O ARG D 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG D 112 " --> pdb=" O ILE D 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN D 90 " --> pdb=" O PHE D 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY D 106 " --> pdb=" O ASP D 94 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N VAL D 96 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR D 104 " --> pdb=" O VAL D 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D 98 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 52 through 56 Processing sheet with id=AB1, first strand: chain 'E' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS E 86 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN E 114 " --> pdb=" O HIS E 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE E 88 " --> pdb=" O ARG E 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG E 112 " --> pdb=" O ILE E 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN E 90 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY E 106 " --> pdb=" O ASP E 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL E 96 " --> pdb=" O TYR E 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR E 104 " --> pdb=" O VAL E 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU E 98 " --> pdb=" O LYS E 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 52 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS F 86 " --> pdb=" O GLN F 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN F 114 " --> pdb=" O HIS F 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE F 88 " --> pdb=" O ARG F 112 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG F 112 " --> pdb=" O ILE F 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN F 90 " --> pdb=" O PHE F 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY F 106 " --> pdb=" O ASP F 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL F 96 " --> pdb=" O TYR F 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR F 104 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU F 98 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 52 through 56 Processing sheet with id=AB5, first strand: chain 'G' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS G 86 " --> pdb=" O GLN G 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN G 114 " --> pdb=" O HIS G 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE G 88 " --> pdb=" O ARG G 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG G 112 " --> pdb=" O ILE G 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN G 90 " --> pdb=" O PHE G 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY G 106 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL G 96 " --> pdb=" O TYR G 104 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N TYR G 104 " --> pdb=" O VAL G 96 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU G 98 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 52 through 56 Processing sheet with id=AB7, first strand: chain 'H' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS H 86 " --> pdb=" O GLN H 114 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLN H 114 " --> pdb=" O HIS H 86 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE H 88 " --> pdb=" O ARG H 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG H 112 " --> pdb=" O ILE H 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN H 90 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY H 106 " --> pdb=" O ASP H 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL H 96 " --> pdb=" O TYR H 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR H 104 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU H 98 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS H 102 " --> pdb=" O LEU H 98 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 52 through 56 Processing sheet with id=AB9, first strand: chain 'I' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS I 86 " --> pdb=" O GLN I 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN I 114 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE I 88 " --> pdb=" O ARG I 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG I 112 " --> pdb=" O ILE I 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN I 90 " --> pdb=" O PHE I 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY I 106 " --> pdb=" O ASP I 94 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL I 96 " --> pdb=" O TYR I 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR I 104 " --> pdb=" O VAL I 96 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU I 98 " --> pdb=" O LYS I 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS I 102 " --> pdb=" O LEU I 98 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 52 through 56 Processing sheet with id=AC2, first strand: chain 'J' and resid 84 through 99 removed outlier: 5.378A pdb=" N HIS J 86 " --> pdb=" O GLN J 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN J 114 " --> pdb=" O HIS J 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE J 88 " --> pdb=" O ARG J 112 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG J 112 " --> pdb=" O ILE J 88 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN J 90 " --> pdb=" O PHE J 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY J 106 " --> pdb=" O ASP J 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL J 96 " --> pdb=" O TYR J 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR J 104 " --> pdb=" O VAL J 96 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU J 98 " --> pdb=" O LYS J 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS J 102 " --> pdb=" O LEU J 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 52 through 56 Processing sheet with id=AC4, first strand: chain 'K' and resid 84 through 99 removed outlier: 5.379A pdb=" N HIS K 86 " --> pdb=" O GLN K 114 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLN K 114 " --> pdb=" O HIS K 86 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ILE K 88 " --> pdb=" O ARG K 112 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG K 112 " --> pdb=" O ILE K 88 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN K 90 " --> pdb=" O PHE K 110 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY K 106 " --> pdb=" O ASP K 94 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N VAL K 96 " --> pdb=" O TYR K 104 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N TYR K 104 " --> pdb=" O VAL K 96 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU K 98 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS K 102 " --> pdb=" O LEU K 98 " (cutoff:3.500A) 761 hydrogen bonds defined for protein. 2250 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 4.23 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 29.040 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.540 ------------------------------------------------------------------------------- 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= 0.168 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.586 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: 0.2504 time to fit residues: 155.5732 Evaluate side-chains 287 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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= 0.244 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 *********************** 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 fitting. rotamer outliers: 50 poor density : 360 time to evaluate : 1.653 Fit side-chains revert: symmetry clash REVERT: A 52 ILE cc_start: 0.7608 (mp) cc_final: 0.7227 (mp) REVERT: A 62 LYS cc_start: 0.7322 (tttt) cc_final: 0.6376 (tppp) REVERT: A 139 LEU cc_start: 0.9044 (mm) cc_final: 0.8822 (mm) REVERT: A 195 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7518 (t0) REVERT: B 62 LYS cc_start: 0.7156 (tttt) cc_final: 0.6515 (ttpt) REVERT: B 117 ASP cc_start: 0.8500 (p0) cc_final: 0.8201 (p0) REVERT: B 195 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7719 (t0) REVERT: C 126 TYR cc_start: 0.8139 (t80) cc_final: 0.7888 (t80) REVERT: C 195 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8006 (t0) REVERT: D 139 LEU cc_start: 0.8964 (mm) cc_final: 0.8737 (mm) REVERT: E 149 ASP cc_start: 0.8486 (m-30) cc_final: 0.8269 (m-30) REVERT: F 97 ASP cc_start: 0.7401 (m-30) cc_final: 0.7196 (m-30) REVERT: F 139 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8776 (mm) REVERT: F 195 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7237 (t0) REVERT: G 37 GLN cc_start: 0.7953 (mt0) cc_final: 0.7664 (mm-40) REVERT: G 166 ILE cc_start: 0.8108 (tp) cc_final: 0.7890 (tp) REVERT: G 195 ASP cc_start: 0.7882 (OUTLIER) cc_final: 0.7674 (t0) REVERT: H 91 GLN cc_start: 0.8560 (tt0) cc_final: 0.8337 (tt0) REVERT: H 126 TYR cc_start: 0.8177 (t80) cc_final: 0.7954 (t80) REVERT: H 195 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7476 (t0) REVERT: H 197 GLU cc_start: 0.5582 (mm-30) cc_final: 0.5307 (mm-30) REVERT: I 195 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7618 (t0) REVERT: J 62 LYS cc_start: 0.6826 (tttt) cc_final: 0.6367 (tppt) REVERT: J 195 ASP cc_start: 0.8113 (OUTLIER) cc_final: 0.7632 (t0) REVERT: K 62 LYS cc_start: 0.7213 (tttt) cc_final: 0.6494 (tppp) REVERT: K 195 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.7966 (t0) outliers start: 50 outliers final: 16 residues processed: 389 average time/residue: 0.2549 time to fit residues: 152.3440 Evaluate side-chains 322 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 296 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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 G residue 195 ASP Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 195 ASP Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 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 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 194 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 178 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 30 GLN B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 99 ASN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 91 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 37 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16214 Z= 0.256 Angle : 0.516 6.935 21791 Z= 0.278 Chirality : 0.044 0.237 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.728 16.355 2255 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.67 % Allowed : 20.14 % 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: 0.88 (0.18), residues: 2002 helix: 1.26 (0.18), residues: 781 sheet: 0.88 (0.25), residues: 484 loop : -0.27 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 84 HIS 0.005 0.001 HIS K 86 PHE 0.013 0.001 PHE J 110 TYR 0.020 0.002 TYR G 36 ARG 0.002 0.000 ARG A 70 *********************** 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 410 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 365 time to evaluate : 1.650 Fit side-chains REVERT: A 45 GLN cc_start: 0.8538 (pm20) cc_final: 0.8238 (pm20) REVERT: A 62 LYS cc_start: 0.7277 (tttt) cc_final: 0.6346 (tppp) REVERT: A 195 ASP cc_start: 0.8245 (OUTLIER) cc_final: 0.7777 (t0) REVERT: A 197 GLU cc_start: 0.6887 (mt-10) cc_final: 0.6549 (mt-10) REVERT: B 62 LYS cc_start: 0.7249 (tttt) cc_final: 0.6628 (ttpt) REVERT: B 117 ASP cc_start: 0.8482 (p0) cc_final: 0.8211 (p0) REVERT: B 139 LEU cc_start: 0.8955 (mm) cc_final: 0.8646 (mm) REVERT: C 78 MET cc_start: 0.8829 (tpp) cc_final: 0.8353 (tpp) REVERT: C 126 TYR cc_start: 0.8136 (t80) cc_final: 0.7802 (t80) REVERT: C 139 LEU cc_start: 0.8984 (mm) cc_final: 0.8776 (mm) REVERT: D 62 LYS cc_start: 0.7138 (tttt) cc_final: 0.6513 (tppt) REVERT: E 97 ASP cc_start: 0.7617 (m-30) cc_final: 0.7368 (m-30) REVERT: E 149 ASP cc_start: 0.8688 (m-30) cc_final: 0.8483 (m-30) REVERT: F 97 ASP cc_start: 0.7384 (m-30) cc_final: 0.7179 (m-30) REVERT: G 37 GLN cc_start: 0.7947 (mt0) cc_final: 0.7675 (mm-40) REVERT: G 126 TYR cc_start: 0.8236 (t80) cc_final: 0.8033 (t80) REVERT: G 139 LEU cc_start: 0.8871 (mm) cc_final: 0.8583 (mm) REVERT: G 195 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7652 (t0) REVERT: H 78 MET cc_start: 0.8756 (tpp) cc_final: 0.8540 (tpp) REVERT: H 91 GLN cc_start: 0.8641 (tt0) cc_final: 0.8406 (tt0) REVERT: I 139 LEU cc_start: 0.9110 (mm) cc_final: 0.8901 (mm) REVERT: J 62 LYS cc_start: 0.6746 (tttt) cc_final: 0.6284 (tppt) REVERT: J 195 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7499 (t0) REVERT: K 45 GLN cc_start: 0.8474 (pm20) cc_final: 0.7682 (pm20) REVERT: K 62 LYS cc_start: 0.7274 (tttt) cc_final: 0.6491 (tppp) REVERT: K 77 GLU cc_start: 0.7030 (pt0) cc_final: 0.6819 (pt0) REVERT: K 139 LEU cc_start: 0.9103 (mm) cc_final: 0.8876 (mm) REVERT: K 195 ASP cc_start: 0.8299 (OUTLIER) cc_final: 0.7906 (t0) REVERT: K 197 GLU cc_start: 0.6477 (mt-10) cc_final: 0.6132 (mt-10) outliers start: 45 outliers final: 28 residues processed: 391 average time/residue: 0.2471 time to fit residues: 148.0513 Evaluate side-chains 335 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 303 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 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 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 G residue 195 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP 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: 9.9990 chunk 135 optimal weight: 6.9990 chunk 93 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 191 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 171 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 HIS C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 121 HIS E 99 ASN E 121 HIS ** 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 30 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16214 Z= 0.277 Angle : 0.527 11.292 21791 Z= 0.284 Chirality : 0.044 0.159 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.814 15.424 2255 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.55 % Allowed : 21.93 % Favored : 75.52 % 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: 0.89 (0.18), residues: 2002 helix: 1.41 (0.18), residues: 781 sheet: 0.87 (0.25), residues: 484 loop : -0.41 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 84 HIS 0.006 0.001 HIS E 121 PHE 0.013 0.002 PHE C 110 TYR 0.025 0.002 TYR G 36 ARG 0.002 0.000 ARG C 44 *********************** 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 366 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 323 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8497 (pm20) cc_final: 0.8285 (pm20) REVERT: A 62 LYS cc_start: 0.7278 (tttt) cc_final: 0.6358 (tppp) REVERT: A 139 LEU cc_start: 0.9124 (mm) cc_final: 0.8861 (mm) REVERT: A 195 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7793 (t0) REVERT: B 62 LYS cc_start: 0.7454 (tttt) cc_final: 0.6827 (ttpt) REVERT: B 117 ASP cc_start: 0.8437 (p0) cc_final: 0.8129 (p0) REVERT: C 78 MET cc_start: 0.8766 (tpp) cc_final: 0.8427 (tpp) REVERT: C 126 TYR cc_start: 0.8166 (t80) cc_final: 0.7883 (t80) REVERT: C 139 LEU cc_start: 0.9053 (mm) cc_final: 0.8844 (mm) REVERT: C 175 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7279 (mt) REVERT: D 62 LYS cc_start: 0.6936 (tttt) cc_final: 0.6441 (tppt) REVERT: E 45 GLN cc_start: 0.8654 (pm20) cc_final: 0.8402 (pm20) REVERT: E 97 ASP cc_start: 0.7660 (m-30) cc_final: 0.7431 (m-30) REVERT: E 149 ASP cc_start: 0.8707 (m-30) cc_final: 0.8490 (m-30) REVERT: G 37 GLN cc_start: 0.7904 (mt0) cc_final: 0.7609 (mm-40) REVERT: H 78 MET cc_start: 0.8803 (tpp) cc_final: 0.8572 (tpp) REVERT: H 91 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: H 149 ASP cc_start: 0.8533 (m-30) cc_final: 0.8318 (m-30) REVERT: J 62 LYS cc_start: 0.6694 (tttt) cc_final: 0.6247 (tppt) REVERT: K 62 LYS cc_start: 0.7197 (tttt) cc_final: 0.6583 (tppp) REVERT: K 195 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7820 (t0) outliers start: 43 outliers final: 25 residues processed: 347 average time/residue: 0.2292 time to fit residues: 124.1016 Evaluate side-chains 305 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 276 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 64 CYS Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU 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 91 GLN Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 195 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 30.0000 chunk 108 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16214 Z= 0.221 Angle : 0.499 12.078 21791 Z= 0.269 Chirality : 0.044 0.221 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.720 14.265 2255 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.50 % Allowed : 21.57 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.18), residues: 2002 helix: 1.55 (0.18), residues: 781 sheet: 0.89 (0.25), residues: 484 loop : -0.35 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 84 HIS 0.004 0.001 HIS C 121 PHE 0.011 0.001 PHE C 110 TYR 0.025 0.002 TYR G 36 ARG 0.002 0.000 ARG C 44 *********************** 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 359 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 317 time to evaluate : 1.695 Fit side-chains REVERT: A 45 GLN cc_start: 0.8477 (pm20) cc_final: 0.8241 (pm20) REVERT: A 62 LYS cc_start: 0.7288 (tttt) cc_final: 0.6340 (tppp) REVERT: A 139 LEU cc_start: 0.9099 (mm) cc_final: 0.8830 (mm) REVERT: A 171 TYR cc_start: 0.7237 (t80) cc_final: 0.7017 (t80) REVERT: A 195 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7717 (t0) REVERT: B 62 LYS cc_start: 0.7479 (tttt) cc_final: 0.6587 (tppp) REVERT: B 117 ASP cc_start: 0.8433 (p0) cc_final: 0.8158 (p0) REVERT: B 175 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7316 (mt) REVERT: C 78 MET cc_start: 0.8722 (tpp) cc_final: 0.8416 (tpp) REVERT: C 126 TYR cc_start: 0.8247 (t80) cc_final: 0.7983 (t80) REVERT: C 197 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6832 (mt-10) REVERT: D 45 GLN cc_start: 0.8478 (pm20) cc_final: 0.8244 (pm20) REVERT: D 62 LYS cc_start: 0.6970 (tttt) cc_final: 0.6350 (tppt) REVERT: E 97 ASP cc_start: 0.7630 (m-30) cc_final: 0.7398 (m-30) REVERT: E 149 ASP cc_start: 0.8695 (m-30) cc_final: 0.8444 (m-30) REVERT: F 171 TYR cc_start: 0.7207 (t80) cc_final: 0.6928 (t80) REVERT: G 37 GLN cc_start: 0.7958 (mt0) cc_final: 0.7639 (mm-40) REVERT: G 139 LEU cc_start: 0.8939 (mm) cc_final: 0.8559 (mm) REVERT: H 62 LYS cc_start: 0.7020 (tttt) cc_final: 0.6333 (tppt) REVERT: H 91 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.8381 (tt0) REVERT: H 149 ASP cc_start: 0.8511 (m-30) cc_final: 0.8250 (m-30) REVERT: J 62 LYS cc_start: 0.6795 (tttt) cc_final: 0.6371 (tppt) REVERT: K 62 LYS cc_start: 0.7172 (tttt) cc_final: 0.6584 (tppp) outliers start: 42 outliers final: 27 residues processed: 340 average time/residue: 0.2390 time to fit residues: 126.5583 Evaluate side-chains 316 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 286 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 91 GLN Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 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 64 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 7.9990 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 16214 Z= 0.481 Angle : 0.656 12.402 21791 Z= 0.351 Chirality : 0.050 0.290 2299 Planarity : 0.004 0.025 2882 Dihedral : 4.320 16.830 2255 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.15 % Allowed : 21.15 % Favored : 75.70 % 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: 0.29 (0.18), residues: 2002 helix: 1.07 (0.17), residues: 781 sheet: 0.70 (0.28), residues: 385 loop : -0.86 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 84 HIS 0.012 0.002 HIS K 121 PHE 0.015 0.002 PHE F 110 TYR 0.034 0.003 TYR G 36 ARG 0.004 0.000 ARG G 112 *********************** 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 365 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 312 time to evaluate : 1.753 Fit side-chains REVERT: A 171 TYR cc_start: 0.7155 (t80) cc_final: 0.6895 (t80) REVERT: A 195 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7840 (t0) REVERT: B 62 LYS cc_start: 0.7451 (tttt) cc_final: 0.6888 (ttpt) REVERT: B 139 LEU cc_start: 0.8877 (mm) cc_final: 0.8650 (mm) REVERT: B 175 LEU cc_start: 0.7627 (OUTLIER) cc_final: 0.7358 (mt) REVERT: B 195 ASP cc_start: 0.8451 (t0) cc_final: 0.8205 (m-30) REVERT: C 78 MET cc_start: 0.8755 (tpp) cc_final: 0.8511 (tpp) REVERT: C 196 LEU cc_start: 0.8009 (tp) cc_final: 0.7795 (tp) REVERT: D 37 GLN cc_start: 0.7868 (mt0) cc_final: 0.7652 (mt0) REVERT: D 62 LYS cc_start: 0.6853 (tttt) cc_final: 0.6260 (tppt) REVERT: E 97 ASP cc_start: 0.7736 (m-30) cc_final: 0.7500 (m-30) REVERT: E 139 LEU cc_start: 0.9101 (mm) cc_final: 0.8898 (mm) REVERT: E 149 ASP cc_start: 0.8794 (m-30) cc_final: 0.8583 (m-30) REVERT: F 117 ASP cc_start: 0.8275 (p0) cc_final: 0.7948 (p0) REVERT: F 171 TYR cc_start: 0.7370 (t80) cc_final: 0.7161 (t80) REVERT: G 37 GLN cc_start: 0.8013 (mt0) cc_final: 0.7653 (mm-40) REVERT: G 62 LYS cc_start: 0.6980 (tttt) cc_final: 0.6546 (tppt) REVERT: G 139 LEU cc_start: 0.9003 (mm) cc_final: 0.8645 (mm) REVERT: H 62 LYS cc_start: 0.6998 (tttt) cc_final: 0.6481 (tppt) REVERT: H 91 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8578 (tt0) REVERT: H 149 ASP cc_start: 0.8691 (m-30) cc_final: 0.8440 (m-30) REVERT: H 175 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7358 (mt) REVERT: H 195 ASP cc_start: 0.8408 (t70) cc_final: 0.8125 (t70) REVERT: I 139 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8806 (mm) REVERT: K 62 LYS cc_start: 0.7206 (tttt) cc_final: 0.6799 (ttpt) outliers start: 53 outliers final: 37 residues processed: 346 average time/residue: 0.2415 time to fit residues: 128.0836 Evaluate side-chains 319 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 108 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 166 ILE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 108 CYS Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 91 GLN Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 108 CYS Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 139 LEU Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 90 GLN Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 109 optimal weight: 0.8980 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 91 GLN G 99 ASN H 76 ASN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN J 99 ASN ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 16214 Z= 0.157 Angle : 0.494 12.972 21791 Z= 0.264 Chirality : 0.044 0.239 2299 Planarity : 0.003 0.027 2882 Dihedral : 3.756 13.854 2255 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.32 % Allowed : 22.88 % Favored : 74.81 % 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: 0.99 (0.18), residues: 2002 helix: 1.54 (0.18), residues: 781 sheet: 0.89 (0.25), residues: 473 loop : -0.37 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP J 84 HIS 0.003 0.001 HIS A 86 PHE 0.008 0.001 PHE B 110 TYR 0.030 0.002 TYR D 171 ARG 0.002 0.000 ARG J 44 *********************** 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 377 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 338 time to evaluate : 1.866 Fit side-chains revert: symmetry clash REVERT: A 45 GLN cc_start: 0.8493 (pm20) cc_final: 0.8242 (pm20) REVERT: A 139 LEU cc_start: 0.9141 (mm) cc_final: 0.8863 (mm) REVERT: A 195 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7642 (t0) REVERT: B 62 LYS cc_start: 0.7254 (tttt) cc_final: 0.6459 (tppp) REVERT: B 117 ASP cc_start: 0.8138 (p0) cc_final: 0.7928 (p0) REVERT: C 78 MET cc_start: 0.8702 (tpp) cc_final: 0.8485 (tpp) REVERT: C 126 TYR cc_start: 0.8220 (t80) cc_final: 0.7914 (t80) REVERT: C 139 LEU cc_start: 0.8981 (mm) cc_final: 0.8731 (mm) REVERT: C 171 TYR cc_start: 0.6936 (t80) cc_final: 0.6637 (t80) REVERT: C 197 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6802 (tt0) REVERT: D 62 LYS cc_start: 0.6896 (tttt) cc_final: 0.6313 (tppt) REVERT: D 78 MET cc_start: 0.8732 (tpp) cc_final: 0.8478 (mmm) REVERT: E 78 MET cc_start: 0.8574 (tpp) cc_final: 0.8341 (tpp) REVERT: E 97 ASP cc_start: 0.7625 (m-30) cc_final: 0.7402 (m-30) REVERT: E 139 LEU cc_start: 0.9081 (mm) cc_final: 0.8866 (mm) REVERT: F 45 GLN cc_start: 0.8429 (pm20) cc_final: 0.8194 (pm20) REVERT: F 117 ASP cc_start: 0.8110 (p0) cc_final: 0.7781 (p0) REVERT: F 201 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7461 (mm-30) REVERT: G 62 LYS cc_start: 0.6754 (tttt) cc_final: 0.6387 (tppt) REVERT: G 139 LEU cc_start: 0.8976 (mm) cc_final: 0.8612 (mm) REVERT: H 45 GLN cc_start: 0.8524 (pm20) cc_final: 0.8293 (pm20) REVERT: H 62 LYS cc_start: 0.7003 (tttt) cc_final: 0.6359 (tppt) REVERT: H 91 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8314 (tt0) REVERT: H 149 ASP cc_start: 0.8652 (m-30) cc_final: 0.8429 (m-30) REVERT: I 139 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8847 (mm) REVERT: K 62 LYS cc_start: 0.7151 (tttt) cc_final: 0.6480 (tppp) outliers start: 39 outliers final: 24 residues processed: 360 average time/residue: 0.2307 time to fit residues: 129.8147 Evaluate side-chains 321 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 294 time to evaluate : 1.729 ------------------------------------------------------------------------------- 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 166 ILE Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 64 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain 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 91 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 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 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 30 GLN C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 30 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 91 GLN G 99 ASN I 30 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 91 GLN ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16214 Z= 0.205 Angle : 0.512 12.673 21791 Z= 0.275 Chirality : 0.044 0.193 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.700 12.904 2255 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.90 % Allowed : 23.11 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.19), residues: 2002 helix: 1.56 (0.18), residues: 781 sheet: 0.84 (0.25), residues: 484 loop : -0.35 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 84 HIS 0.004 0.001 HIS A 86 PHE 0.011 0.001 PHE B 110 TYR 0.033 0.001 TYR F 171 ARG 0.003 0.000 ARG E 44 *********************** 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 335 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 303 time to evaluate : 1.757 Fit side-chains REVERT: A 139 LEU cc_start: 0.9132 (mm) cc_final: 0.8874 (mm) REVERT: A 197 GLU cc_start: 0.7248 (mt-10) cc_final: 0.6803 (mt-10) REVERT: B 62 LYS cc_start: 0.7238 (tttt) cc_final: 0.6448 (tppp) REVERT: B 78 MET cc_start: 0.8730 (tpp) cc_final: 0.8331 (mmm) REVERT: B 117 ASP cc_start: 0.8181 (p0) cc_final: 0.7958 (p0) REVERT: C 78 MET cc_start: 0.8650 (tpp) cc_final: 0.8437 (tpp) REVERT: C 126 TYR cc_start: 0.8211 (t80) cc_final: 0.7939 (t80) REVERT: D 62 LYS cc_start: 0.6895 (tttt) cc_final: 0.6339 (tppt) REVERT: D 78 MET cc_start: 0.8733 (tpp) cc_final: 0.8452 (mmm) REVERT: E 56 MET cc_start: 0.5025 (ttm) cc_final: 0.4823 (ttm) REVERT: E 97 ASP cc_start: 0.7611 (m-30) cc_final: 0.7386 (m-30) REVERT: E 139 LEU cc_start: 0.9070 (mm) cc_final: 0.8850 (mm) REVERT: F 117 ASP cc_start: 0.8118 (p0) cc_final: 0.7810 (p0) REVERT: G 62 LYS cc_start: 0.6779 (tttt) cc_final: 0.6397 (tppt) REVERT: G 139 LEU cc_start: 0.8974 (mm) cc_final: 0.8611 (mm) REVERT: H 62 LYS cc_start: 0.6993 (tttt) cc_final: 0.6359 (tppt) REVERT: H 91 GLN cc_start: 0.8562 (tt0) cc_final: 0.8360 (tt0) REVERT: H 149 ASP cc_start: 0.8632 (m-30) cc_final: 0.8392 (m-30) REVERT: I 139 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8830 (mm) REVERT: J 62 LYS cc_start: 0.6428 (tttt) cc_final: 0.6018 (tppt) REVERT: K 62 LYS cc_start: 0.7159 (tttt) cc_final: 0.6528 (tppp) outliers start: 32 outliers final: 25 residues processed: 319 average time/residue: 0.2359 time to fit residues: 117.4940 Evaluate side-chains 314 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 288 time to evaluate : 1.709 ------------------------------------------------------------------------------- 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 166 ILE 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 D residue 64 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU 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 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 177 optimal weight: 40.0000 chunk 107 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 139 optimal weight: 0.0370 chunk 54 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.5864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 91 GLN G 99 ASN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16214 Z= 0.215 Angle : 0.514 12.925 21791 Z= 0.277 Chirality : 0.045 0.178 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.713 13.133 2255 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 22.99 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2002 helix: 1.55 (0.18), residues: 781 sheet: 0.62 (0.25), residues: 506 loop : -0.28 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 84 HIS 0.004 0.001 HIS J 121 PHE 0.011 0.001 PHE B 110 TYR 0.029 0.002 TYR F 171 ARG 0.002 0.000 ARG F 44 *********************** 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 338 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 304 time to evaluate : 1.740 Fit side-chains REVERT: A 139 LEU cc_start: 0.9129 (mm) cc_final: 0.8888 (mm) REVERT: B 62 LYS cc_start: 0.7247 (tttt) cc_final: 0.6461 (tppp) REVERT: B 78 MET cc_start: 0.8751 (tpp) cc_final: 0.8298 (mmm) REVERT: C 78 MET cc_start: 0.8654 (tpp) cc_final: 0.8446 (tpp) REVERT: C 126 TYR cc_start: 0.8228 (t80) cc_final: 0.7959 (t80) REVERT: C 197 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6581 (tt0) REVERT: D 62 LYS cc_start: 0.6888 (tttt) cc_final: 0.6320 (tppt) REVERT: D 78 MET cc_start: 0.8742 (tpp) cc_final: 0.8498 (mmm) REVERT: E 56 MET cc_start: 0.5024 (ttm) cc_final: 0.4792 (ttm) REVERT: E 78 MET cc_start: 0.8560 (tpp) cc_final: 0.8331 (tpp) REVERT: E 97 ASP cc_start: 0.7605 (m-30) cc_final: 0.7382 (m-30) REVERT: E 139 LEU cc_start: 0.9073 (mm) cc_final: 0.8860 (mm) REVERT: F 45 GLN cc_start: 0.8331 (pm20) cc_final: 0.7998 (pm20) REVERT: F 117 ASP cc_start: 0.8089 (p0) cc_final: 0.7827 (p0) REVERT: G 62 LYS cc_start: 0.6697 (tttt) cc_final: 0.6341 (tppt) REVERT: G 139 LEU cc_start: 0.8970 (mm) cc_final: 0.8603 (mm) REVERT: H 62 LYS cc_start: 0.6950 (tttt) cc_final: 0.6477 (tppt) REVERT: H 149 ASP cc_start: 0.8616 (m-30) cc_final: 0.8359 (m-30) REVERT: I 139 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8822 (mm) REVERT: J 62 LYS cc_start: 0.6442 (tttt) cc_final: 0.6028 (tppt) REVERT: K 62 LYS cc_start: 0.7020 (tttt) cc_final: 0.6373 (tppp) outliers start: 34 outliers final: 26 residues processed: 324 average time/residue: 0.2329 time to fit residues: 117.4230 Evaluate side-chains 312 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 285 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 166 ILE 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 D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU 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 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 130 optimal weight: 0.5980 chunk 197 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** H 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 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 16214 Z= 0.422 Angle : 0.628 13.039 21791 Z= 0.338 Chirality : 0.049 0.213 2299 Planarity : 0.004 0.024 2882 Dihedral : 4.196 15.030 2255 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.66 % Allowed : 22.88 % Favored : 75.46 % 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: 0.37 (0.18), residues: 2002 helix: 1.19 (0.18), residues: 781 sheet: 0.18 (0.24), residues: 517 loop : -0.67 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 84 HIS 0.009 0.002 HIS K 121 PHE 0.016 0.002 PHE F 110 TYR 0.035 0.002 TYR B 171 ARG 0.003 0.000 ARG E 44 ********************** 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 312 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 284 time to evaluate : 2.029 Fit side-chains REVERT: A 45 GLN cc_start: 0.8500 (pm20) cc_final: 0.8250 (pm20) REVERT: A 139 LEU cc_start: 0.9159 (mm) cc_final: 0.8938 (mm) REVERT: B 62 LYS cc_start: 0.7278 (tttt) cc_final: 0.6484 (tppp) REVERT: B 139 LEU cc_start: 0.8872 (mm) cc_final: 0.8632 (mm) REVERT: C 78 MET cc_start: 0.8736 (tpp) cc_final: 0.8500 (tpp) REVERT: C 171 TYR cc_start: 0.7197 (t80) cc_final: 0.6779 (t80) REVERT: C 197 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6878 (mt-10) REVERT: E 56 MET cc_start: 0.5135 (ttm) cc_final: 0.4929 (ttm) REVERT: E 97 ASP cc_start: 0.7779 (m-30) cc_final: 0.7549 (m-30) REVERT: F 117 ASP cc_start: 0.8254 (p0) cc_final: 0.8000 (p0) REVERT: F 201 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7253 (mm-30) REVERT: G 62 LYS cc_start: 0.6788 (tttt) cc_final: 0.6301 (tppt) REVERT: G 91 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: G 139 LEU cc_start: 0.9019 (mm) cc_final: 0.8653 (mm) REVERT: H 62 LYS cc_start: 0.6998 (tttt) cc_final: 0.6499 (tppt) REVERT: H 149 ASP cc_start: 0.8650 (m-30) cc_final: 0.8383 (m-30) REVERT: I 139 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8805 (mm) REVERT: K 62 LYS cc_start: 0.7008 (tttt) cc_final: 0.6423 (tppt) outliers start: 28 outliers final: 23 residues processed: 298 average time/residue: 0.2332 time to fit residues: 109.1468 Evaluate side-chains 296 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 271 time to evaluate : 1.740 ------------------------------------------------------------------------------- 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 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 D residue 175 LEU Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 108 CYS Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU 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 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 144 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 8.9990 chunk 19 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 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 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 ** 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 = 0.3896 r_free = 0.3896 target = 0.172659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.128661 restraints weight = 19187.735| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.46 r_work: 0.3227 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16214 Z= 0.181 Angle : 0.510 13.115 21791 Z= 0.275 Chirality : 0.045 0.164 2299 Planarity : 0.003 0.027 2882 Dihedral : 3.771 13.875 2255 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.60 % Allowed : 23.59 % Favored : 74.81 % 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: 0.89 (0.19), residues: 2002 helix: 1.55 (0.18), residues: 781 sheet: 0.52 (0.25), residues: 506 loop : -0.34 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 84 HIS 0.003 0.001 HIS K 121 PHE 0.010 0.001 PHE C 110 TYR 0.038 0.002 TYR H 171 ARG 0.001 0.000 ARG E 112 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3425.02 seconds wall clock time: 62 minutes 6.34 seconds (3726.34 seconds total)