Starting phenix.real_space_refine on Fri Feb 16 17:07:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/02_2024/8h1p_34430.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/02_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_34430/02_2024/8h1p_34430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/02_2024/8h1p_34430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/02_2024/8h1p_34430.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/02_2024/8h1p_34430.pdb" } 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 Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15950 Number of models: 1 Model: "" Number of chains: 11 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} Chain: "B" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "C" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "D" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "E" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "F" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "G" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "I" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "J" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Chain: "K" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1450 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 4, 'TRANS': 179} Time building chain proxies: 9.11, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 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: 5.72 Conformation dependent library (CDL) restraints added in 3.2 seconds 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3674 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 22 sheets defined 41.9% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 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: 4.27 Time building geometry restraints manager: 6.19 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: 100.70 - 107.35: 276 107.35 - 114.01: 8792 114.01 - 120.67: 6922 120.67 - 127.32: 5724 127.32 - 133.98: 77 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 2.520 nonbonded pdb=" OD1 ASP J 195 " pdb=" OH TYR K 51 " model vdw 2.223 2.440 nonbonded pdb=" OD1 ASP I 195 " pdb=" OH TYR J 51 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR A 51 " pdb=" OD1 ASP K 195 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP G 195 " pdb=" OH TYR H 51 " model vdw 2.248 2.440 ... (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 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: 0.370 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: 2.680 Check model and map are aligned: 0.260 Set scattering table: 0.190 Process input model: 44.380 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.980 ------------------------------------------------------------------------------- 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 : 2.038 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: 0.2609 time to fit residues: 161.4135 Evaluate side-chains 287 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 1.895 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 92 ASN 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: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16214 Z= 0.242 Angle : 0.522 5.668 21791 Z= 0.282 Chirality : 0.045 0.249 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.698 14.197 2255 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.85 % Allowed : 19.49 % Favored : 77.66 % 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: 0.83 (0.18), residues: 2002 helix: 1.08 (0.17), residues: 770 sheet: 0.77 (0.25), residues: 484 loop : -0.01 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 84 HIS 0.004 0.001 HIS G 86 PHE 0.013 0.001 PHE I 110 TYR 0.016 0.001 TYR B 171 ARG 0.003 0.000 ARG A 70 *********************** 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 402 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 354 time to evaluate : 1.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7327 (tttt) cc_final: 0.6359 (tppp) REVERT: A 139 LEU cc_start: 0.9017 (mm) cc_final: 0.8769 (mm) REVERT: A 195 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7878 (t0) REVERT: B 62 LYS cc_start: 0.7154 (tttt) cc_final: 0.6514 (ttpt) REVERT: B 139 LEU cc_start: 0.8901 (mm) cc_final: 0.8655 (mm) REVERT: B 195 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8060 (t0) REVERT: C 195 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.8061 (t0) REVERT: F 97 ASP cc_start: 0.7386 (m-30) cc_final: 0.7178 (m-30) REVERT: F 139 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8760 (mm) REVERT: F 195 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7261 (t0) REVERT: G 37 GLN cc_start: 0.7966 (mt0) cc_final: 0.7693 (mm-40) REVERT: H 197 GLU cc_start: 0.5498 (mm-30) cc_final: 0.5115 (mm-30) REVERT: I 195 ASP cc_start: 0.8364 (OUTLIER) cc_final: 0.7858 (t0) REVERT: J 62 LYS cc_start: 0.6822 (tttt) cc_final: 0.6365 (tppt) REVERT: J 195 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7692 (t0) REVERT: K 62 LYS cc_start: 0.7210 (tttt) cc_final: 0.6490 (tppp) REVERT: K 195 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.8065 (t70) REVERT: K 197 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6241 (mt-10) outliers start: 48 outliers final: 18 residues processed: 380 average time/residue: 0.2601 time to fit residues: 151.1180 Evaluate side-chains 332 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 306 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 138 SER Chi-restraints excluded: chain C residue 195 ASP Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 138 SER 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 50 GLU Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 123 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: 7.9990 chunk 55 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 180 optimal weight: 7.9990 chunk 194 optimal weight: 0.0060 chunk 160 optimal weight: 7.9990 chunk 178 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 121 HIS E 30 GLN 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 ** 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 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16214 Z= 0.323 Angle : 0.549 6.395 21791 Z= 0.296 Chirality : 0.045 0.262 2299 Planarity : 0.003 0.025 2882 Dihedral : 3.878 16.430 2255 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.85 % Allowed : 20.02 % Favored : 77.12 % 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: 0.60 (0.18), residues: 2002 helix: 1.02 (0.17), residues: 781 sheet: 0.64 (0.24), residues: 495 loop : -0.34 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 84 HIS 0.005 0.002 HIS E 121 PHE 0.016 0.002 PHE I 110 TYR 0.021 0.002 TYR G 36 ARG 0.003 0.000 ARG I 112 *********************** 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 394 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 346 time to evaluate : 1.875 Fit side-chains revert: symmetry clash REVERT: A 62 LYS cc_start: 0.7235 (tttt) cc_final: 0.6292 (tppp) REVERT: A 139 LEU cc_start: 0.9083 (mm) cc_final: 0.8813 (mm) REVERT: A 195 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7972 (t0) REVERT: B 62 LYS cc_start: 0.7234 (tttt) cc_final: 0.6600 (ttpt) REVERT: B 139 LEU cc_start: 0.8930 (mm) cc_final: 0.8689 (mm) REVERT: C 73 ASN cc_start: 0.8164 (m110) cc_final: 0.7875 (m110) REVERT: E 97 ASP cc_start: 0.7601 (m-30) cc_final: 0.7351 (m-30) REVERT: G 37 GLN cc_start: 0.7927 (mt0) cc_final: 0.7654 (mm-40) REVERT: G 139 LEU cc_start: 0.8906 (mm) cc_final: 0.8620 (mm) REVERT: H 145 GLU cc_start: 0.7965 (tt0) cc_final: 0.7723 (tt0) REVERT: H 195 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7428 (t0) REVERT: H 197 GLU cc_start: 0.5712 (mm-30) cc_final: 0.5507 (mm-30) REVERT: I 195 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7794 (t70) REVERT: J 62 LYS cc_start: 0.6694 (tttt) cc_final: 0.6260 (tppt) REVERT: J 195 ASP cc_start: 0.8045 (OUTLIER) cc_final: 0.7691 (t0) REVERT: K 62 LYS cc_start: 0.7278 (tttt) cc_final: 0.6493 (tppp) REVERT: K 195 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7997 (t70) outliers start: 48 outliers final: 30 residues processed: 371 average time/residue: 0.2481 time to fit residues: 139.9855 Evaluate side-chains 347 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 312 time to evaluate : 2.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 195 ASP Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 195 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 195 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 138 SER 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: 4.9990 chunk 135 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 171 optimal weight: 4.9990 chunk 51 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** 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 92 ASN D 99 ASN E 30 GLN E 99 ASN E 121 HIS F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 30 GLN G 92 ASN G 99 ASN H 30 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN ** 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 91 GLN ** 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 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16214 Z= 0.297 Angle : 0.538 11.880 21791 Z= 0.290 Chirality : 0.045 0.210 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.905 15.764 2255 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.33 % Allowed : 21.63 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.18), residues: 2002 helix: 1.19 (0.17), residues: 781 sheet: 0.52 (0.24), residues: 495 loop : -0.48 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 84 HIS 0.007 0.001 HIS C 121 PHE 0.013 0.001 PHE C 110 TYR 0.027 0.002 TYR D 36 ARG 0.002 0.000 ARG J 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 408 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 352 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9128 (mm) cc_final: 0.8846 (mm) REVERT: B 62 LYS cc_start: 0.7449 (tttt) cc_final: 0.6813 (ttpt) REVERT: B 139 LEU cc_start: 0.8958 (mm) cc_final: 0.8729 (mm) REVERT: B 175 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7308 (mt) REVERT: C 139 LEU cc_start: 0.8999 (mm) cc_final: 0.8785 (mm) REVERT: D 62 LYS cc_start: 0.6993 (tttt) cc_final: 0.6415 (tppt) REVERT: E 97 ASP cc_start: 0.7638 (m-30) cc_final: 0.7404 (m-30) REVERT: G 37 GLN cc_start: 0.7899 (mt0) cc_final: 0.7619 (mm-40) REVERT: G 139 LEU cc_start: 0.8976 (mm) cc_final: 0.8667 (mm) REVERT: G 201 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7116 (mm-30) REVERT: J 62 LYS cc_start: 0.6725 (tttt) cc_final: 0.6277 (tppt) REVERT: K 62 LYS cc_start: 0.7200 (tttt) cc_final: 0.6578 (tppp) REVERT: K 195 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7919 (t70) outliers start: 56 outliers final: 30 residues processed: 384 average time/residue: 0.2412 time to fit residues: 141.9085 Evaluate side-chains 325 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 293 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 123 ASP Chi-restraints excluded: chain F residue 138 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain K residue 76 ASN Chi-restraints excluded: chain K residue 89 THR 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: 50.0000 chunk 108 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 99 ASN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 30 GLN G 92 ASN G 99 ASN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN J 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16214 Z= 0.311 Angle : 0.557 11.842 21791 Z= 0.298 Chirality : 0.046 0.279 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.960 15.415 2255 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.09 % Allowed : 21.03 % Favored : 75.88 % 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: 0.62 (0.18), residues: 2002 helix: 1.26 (0.17), residues: 781 sheet: 0.86 (0.28), residues: 385 loop : -0.58 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 84 HIS 0.007 0.002 HIS K 121 PHE 0.012 0.002 PHE F 110 TYR 0.027 0.002 TYR C 171 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 375 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 323 time to evaluate : 1.868 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9143 (mm) cc_final: 0.8889 (mm) REVERT: A 149 ASP cc_start: 0.8606 (m-30) cc_final: 0.8386 (m-30) REVERT: B 62 LYS cc_start: 0.7496 (tttt) cc_final: 0.6577 (tppp) REVERT: B 175 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7321 (mt) REVERT: C 139 LEU cc_start: 0.9029 (mm) cc_final: 0.8824 (mm) REVERT: D 37 GLN cc_start: 0.7905 (mt0) cc_final: 0.7646 (mm-40) REVERT: D 62 LYS cc_start: 0.6896 (tttt) cc_final: 0.6306 (tppt) REVERT: D 145 GLU cc_start: 0.7877 (tt0) cc_final: 0.7677 (tt0) REVERT: E 97 ASP cc_start: 0.7627 (m-30) cc_final: 0.7380 (m-30) REVERT: E 139 LEU cc_start: 0.9110 (mm) cc_final: 0.8866 (mm) REVERT: E 149 ASP cc_start: 0.8617 (m-30) cc_final: 0.8378 (m-30) REVERT: F 171 TYR cc_start: 0.7230 (t80) cc_final: 0.6917 (t80) REVERT: G 37 GLN cc_start: 0.7869 (mt0) cc_final: 0.7449 (mm-40) REVERT: G 62 LYS cc_start: 0.6756 (tttt) cc_final: 0.6320 (tppt) REVERT: G 139 LEU cc_start: 0.9037 (mm) cc_final: 0.8717 (mm) REVERT: G 201 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7073 (mm-30) REVERT: I 139 LEU cc_start: 0.9123 (mm) cc_final: 0.8850 (mm) REVERT: I 175 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7314 (mt) REVERT: J 62 LYS cc_start: 0.6716 (tttt) cc_final: 0.6263 (tppt) REVERT: J 91 GLN cc_start: 0.8717 (tt0) cc_final: 0.8509 (tt0) REVERT: K 62 LYS cc_start: 0.7281 (tttt) cc_final: 0.6615 (tppp) REVERT: K 139 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8902 (mm) REVERT: K 195 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7916 (t70) outliers start: 52 outliers final: 33 residues processed: 354 average time/residue: 0.2445 time to fit residues: 133.2897 Evaluate side-chains 317 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 280 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 138 SER 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 F residue 138 SER 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 G residue 138 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 138 SER 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 175 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain K residue 195 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 112 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 159 optimal weight: 30.0000 chunk 88 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- 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 30 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 30 GLN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 30 GLN G 92 ASN G 99 ASN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 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 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16214 Z= 0.292 Angle : 0.542 12.452 21791 Z= 0.289 Chirality : 0.045 0.219 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.936 15.172 2255 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.09 % Allowed : 21.09 % 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: 0.64 (0.18), residues: 2002 helix: 1.34 (0.18), residues: 781 sheet: 0.48 (0.24), residues: 484 loop : -0.53 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 84 HIS 0.007 0.001 HIS K 121 PHE 0.012 0.001 PHE C 110 TYR 0.028 0.002 TYR A 171 ARG 0.002 0.000 ARG D 44 *********************** 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 362 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 310 time to evaluate : 1.946 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9154 (mm) cc_final: 0.8892 (mm) REVERT: B 62 LYS cc_start: 0.7354 (tttt) cc_final: 0.6500 (tppp) REVERT: B 175 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7392 (mt) REVERT: C 139 LEU cc_start: 0.9033 (mm) cc_final: 0.8807 (mm) REVERT: D 37 GLN cc_start: 0.7814 (mt0) cc_final: 0.7583 (mm-40) REVERT: D 62 LYS cc_start: 0.6877 (tttt) cc_final: 0.6294 (tppt) REVERT: E 56 MET cc_start: 0.5010 (ttm) cc_final: 0.4787 (ttm) REVERT: E 97 ASP cc_start: 0.7669 (m-30) cc_final: 0.7413 (m-30) REVERT: E 139 LEU cc_start: 0.9106 (mm) cc_final: 0.8850 (mm) REVERT: F 171 TYR cc_start: 0.7201 (t80) cc_final: 0.6971 (t80) REVERT: G 37 GLN cc_start: 0.7853 (mt0) cc_final: 0.7486 (mm-40) REVERT: G 62 LYS cc_start: 0.6738 (tttt) cc_final: 0.6359 (tppt) REVERT: G 139 LEU cc_start: 0.9060 (mm) cc_final: 0.8740 (mm) REVERT: G 201 GLU cc_start: 0.7300 (mm-30) cc_final: 0.7028 (mm-30) REVERT: I 139 LEU cc_start: 0.9175 (mm) cc_final: 0.8962 (mm) REVERT: I 175 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7292 (mt) REVERT: J 62 LYS cc_start: 0.6539 (tttt) cc_final: 0.6146 (tppt) REVERT: J 171 TYR cc_start: 0.7257 (t80) cc_final: 0.6807 (t80) REVERT: K 62 LYS cc_start: 0.7348 (tttt) cc_final: 0.6685 (tppp) REVERT: K 139 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8905 (mm) outliers start: 52 outliers final: 38 residues processed: 342 average time/residue: 0.2427 time to fit residues: 127.6784 Evaluate side-chains 323 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 282 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 138 SER 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 108 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 138 SER 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 138 SER 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 F residue 138 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 108 CYS Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 139 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 5.9990 chunk 21 optimal weight: 0.0060 chunk 109 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN E 92 ASN E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 30 GLN G 92 ASN G 99 ASN H 30 GLN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN I 30 GLN ** 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 92 ASN K 30 GLN ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16214 Z= 0.211 Angle : 0.509 12.742 21791 Z= 0.271 Chirality : 0.044 0.224 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.768 13.806 2255 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.73 % Allowed : 20.97 % Favored : 76.29 % 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: 1.54 (0.18), residues: 781 sheet: 0.61 (0.25), residues: 484 loop : -0.38 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 84 HIS 0.004 0.001 HIS J 121 PHE 0.011 0.001 PHE I 110 TYR 0.022 0.002 TYR A 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 361 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 315 time to evaluate : 1.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9131 (mm) cc_final: 0.8859 (mm) REVERT: B 62 LYS cc_start: 0.7250 (tttt) cc_final: 0.6475 (tppp) REVERT: B 175 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7356 (mt) REVERT: B 195 ASP cc_start: 0.8476 (t0) cc_final: 0.8245 (m-30) REVERT: C 139 LEU cc_start: 0.9016 (mm) cc_final: 0.8801 (mm) REVERT: D 37 GLN cc_start: 0.7812 (mt0) cc_final: 0.7596 (mm-40) REVERT: D 45 GLN cc_start: 0.8535 (pm20) cc_final: 0.8283 (pm20) REVERT: D 62 LYS cc_start: 0.6870 (tttt) cc_final: 0.6297 (tppt) REVERT: E 56 MET cc_start: 0.5004 (ttm) cc_final: 0.4788 (ttm) REVERT: E 97 ASP cc_start: 0.7590 (m-30) cc_final: 0.7341 (m-30) REVERT: E 139 LEU cc_start: 0.9081 (mm) cc_final: 0.8848 (mm) REVERT: F 171 TYR cc_start: 0.7193 (t80) cc_final: 0.6983 (t80) REVERT: G 37 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7540 (mm-40) REVERT: G 62 LYS cc_start: 0.6779 (tttt) cc_final: 0.6395 (tppt) REVERT: G 139 LEU cc_start: 0.9065 (mm) cc_final: 0.8715 (mm) REVERT: G 201 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7043 (mm-30) REVERT: I 139 LEU cc_start: 0.9137 (mm) cc_final: 0.8929 (mm) REVERT: J 45 GLN cc_start: 0.8452 (pm20) cc_final: 0.8242 (pm20) REVERT: J 62 LYS cc_start: 0.6489 (tttt) cc_final: 0.6131 (tppt) REVERT: J 171 TYR cc_start: 0.7188 (t80) cc_final: 0.6841 (t80) REVERT: K 62 LYS cc_start: 0.7239 (tttt) cc_final: 0.6558 (tppp) REVERT: K 139 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8911 (mm) REVERT: K 171 TYR cc_start: 0.7055 (t80) cc_final: 0.6799 (t80) outliers start: 46 outliers final: 35 residues processed: 341 average time/residue: 0.2352 time to fit residues: 125.6039 Evaluate side-chains 324 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 287 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 CYS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 138 SER 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 108 CYS Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 138 SER 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 138 SER 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 138 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 89 THR Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 138 SER Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 139 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.9980 chunk 76 optimal weight: 0.0870 chunk 113 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 130 optimal weight: 0.0000 chunk 94 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN E 30 GLN E 91 GLN E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 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** ** K 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16214 Z= 0.141 Angle : 0.476 12.780 21791 Z= 0.254 Chirality : 0.044 0.168 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.550 13.603 2255 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.44 % Allowed : 21.45 % Favored : 76.11 % 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: 1.13 (0.19), residues: 2002 helix: 1.71 (0.18), residues: 792 sheet: 0.80 (0.25), residues: 484 loop : -0.29 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP G 84 HIS 0.002 0.001 HIS J 86 PHE 0.009 0.001 PHE G 110 TYR 0.032 0.001 TYR C 171 ARG 0.002 0.000 ARG C 46 *********************** 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 371 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 330 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9129 (mm) cc_final: 0.8865 (mm) REVERT: A 175 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7233 (mt) REVERT: B 62 LYS cc_start: 0.7241 (tttt) cc_final: 0.6460 (tppp) REVERT: B 175 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7220 (mt) REVERT: B 195 ASP cc_start: 0.8491 (t0) cc_final: 0.8286 (m-30) REVERT: C 139 LEU cc_start: 0.9012 (mm) cc_final: 0.8778 (mm) REVERT: D 62 LYS cc_start: 0.6874 (tttt) cc_final: 0.6320 (tppt) REVERT: D 197 GLU cc_start: 0.6970 (mt-10) cc_final: 0.6240 (tt0) REVERT: E 56 MET cc_start: 0.5133 (ttm) cc_final: 0.4882 (ttm) REVERT: E 97 ASP cc_start: 0.7522 (m-30) cc_final: 0.7288 (m-30) REVERT: E 139 LEU cc_start: 0.9060 (mm) cc_final: 0.8821 (mm) REVERT: F 50 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.7217 (pm20) REVERT: F 171 TYR cc_start: 0.7117 (t80) cc_final: 0.6895 (t80) REVERT: G 37 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.7410 (mm-40) REVERT: G 62 LYS cc_start: 0.6698 (tttt) cc_final: 0.6178 (tppt) REVERT: G 139 LEU cc_start: 0.9066 (mm) cc_final: 0.8763 (mm) REVERT: H 62 LYS cc_start: 0.7210 (tttt) cc_final: 0.6713 (tppt) REVERT: I 139 LEU cc_start: 0.9135 (mm) cc_final: 0.8930 (mm) REVERT: J 62 LYS cc_start: 0.6386 (tttt) cc_final: 0.5953 (tppt) REVERT: K 62 LYS cc_start: 0.7156 (tttt) cc_final: 0.6518 (tppp) REVERT: K 171 TYR cc_start: 0.7045 (t80) cc_final: 0.6842 (t80) outliers start: 41 outliers final: 26 residues processed: 354 average time/residue: 0.2322 time to fit residues: 128.8140 Evaluate side-chains 328 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 298 time to evaluate : 1.822 ------------------------------------------------------------------------------- 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 175 LEU Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 123 ASP Chi-restraints excluded: chain D residue 138 SER 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 138 SER 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 138 SER Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain K residue 89 THR Chi-restraints excluded: chain K residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 177 optimal weight: 50.0000 chunk 107 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 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 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN H 99 ASN ** I 76 ASN ** 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 ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN K 121 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16214 Z= 0.316 Angle : 0.572 13.200 21791 Z= 0.306 Chirality : 0.047 0.178 2299 Planarity : 0.003 0.024 2882 Dihedral : 3.857 13.653 2255 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.26 % Allowed : 21.87 % Favored : 75.88 % 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: 0.86 (0.19), residues: 2002 helix: 1.52 (0.18), residues: 781 sheet: 0.46 (0.24), residues: 506 loop : -0.32 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 84 HIS 0.006 0.001 HIS J 121 PHE 0.014 0.002 PHE C 110 TYR 0.034 0.002 TYR C 171 ARG 0.003 0.000 ARG I 46 *********************** 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 328 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 290 time to evaluate : 1.947 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9132 (mm) cc_final: 0.8880 (mm) REVERT: B 62 LYS cc_start: 0.7286 (tttt) cc_final: 0.6500 (tppp) REVERT: B 175 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7244 (mt) REVERT: C 139 LEU cc_start: 0.8990 (mm) cc_final: 0.8769 (mm) REVERT: D 62 LYS cc_start: 0.6860 (tttt) cc_final: 0.6295 (tppt) REVERT: E 56 MET cc_start: 0.5035 (ttm) cc_final: 0.4822 (ttm) REVERT: E 97 ASP cc_start: 0.7633 (m-30) cc_final: 0.7381 (m-30) REVERT: E 139 LEU cc_start: 0.9105 (mm) cc_final: 0.8884 (mm) REVERT: F 171 TYR cc_start: 0.7209 (t80) cc_final: 0.6990 (t80) REVERT: G 45 GLN cc_start: 0.8378 (pm20) cc_final: 0.8134 (pm20) REVERT: G 62 LYS cc_start: 0.6738 (tttt) cc_final: 0.6269 (tppt) REVERT: G 139 LEU cc_start: 0.9069 (mm) cc_final: 0.8777 (mm) REVERT: H 62 LYS cc_start: 0.7246 (tttt) cc_final: 0.6680 (ttpt) REVERT: J 62 LYS cc_start: 0.6413 (tttt) cc_final: 0.6022 (tppt) REVERT: J 171 TYR cc_start: 0.7210 (t80) cc_final: 0.6728 (t80) REVERT: K 62 LYS cc_start: 0.7062 (tttt) cc_final: 0.6770 (ttpt) REVERT: K 171 TYR cc_start: 0.7067 (t80) cc_final: 0.6809 (t80) outliers start: 38 outliers final: 33 residues processed: 311 average time/residue: 0.2426 time to fit residues: 117.2111 Evaluate side-chains 310 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 276 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 138 SER Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 138 SER 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 D residue 138 SER 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 138 SER 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 138 SER Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 138 SER Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 138 SER 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: 0.9980 chunk 114 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 121 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 ** 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 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 30 GLN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 91 GLN K 99 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3672 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= 0.171 Angle : 0.508 13.178 21791 Z= 0.271 Chirality : 0.044 0.170 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.639 13.093 2255 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.02 % Allowed : 22.28 % 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: 1.08 (0.19), residues: 2002 helix: 1.68 (0.18), residues: 781 sheet: 0.58 (0.24), residues: 506 loop : -0.16 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP G 84 HIS 0.003 0.001 HIS J 121 PHE 0.010 0.001 PHE I 110 TYR 0.031 0.001 TYR C 171 ARG 0.002 0.000 ARG D 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 339 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 305 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9119 (mm) cc_final: 0.8864 (mm) REVERT: B 45 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: B 62 LYS cc_start: 0.7267 (tttt) cc_final: 0.6474 (tppp) REVERT: B 175 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7050 (mt) REVERT: C 139 LEU cc_start: 0.9003 (mm) cc_final: 0.8767 (mm) REVERT: D 62 LYS cc_start: 0.6850 (tttt) cc_final: 0.6285 (tppt) REVERT: D 197 GLU cc_start: 0.6971 (mt-10) cc_final: 0.6226 (tt0) REVERT: E 56 MET cc_start: 0.5059 (ttm) cc_final: 0.4830 (ttm) REVERT: E 97 ASP cc_start: 0.7550 (m-30) cc_final: 0.7311 (m-30) REVERT: E 139 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8843 (mm) REVERT: F 171 TYR cc_start: 0.7081 (t80) cc_final: 0.6848 (t80) REVERT: G 45 GLN cc_start: 0.8399 (pm20) cc_final: 0.8065 (pm20) REVERT: G 62 LYS cc_start: 0.6743 (tttt) cc_final: 0.6210 (tppt) REVERT: G 139 LEU cc_start: 0.9056 (mm) cc_final: 0.8723 (mm) REVERT: J 62 LYS cc_start: 0.6530 (tttt) cc_final: 0.6132 (tppt) REVERT: J 171 TYR cc_start: 0.7080 (t80) cc_final: 0.6751 (t80) REVERT: K 62 LYS cc_start: 0.7021 (tttt) cc_final: 0.6387 (tppp) REVERT: K 171 TYR cc_start: 0.7070 (t80) cc_final: 0.6842 (t80) outliers start: 34 outliers final: 28 residues processed: 324 average time/residue: 0.2310 time to fit residues: 117.6097 Evaluate side-chains 318 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 287 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 108 CYS Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 45 GLN Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 138 SER 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 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 139 LEU 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 123 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 123 ASP Chi-restraints excluded: chain H residue 196 LEU Chi-restraints excluded: chain I residue 89 THR Chi-restraints excluded: chain I residue 123 ASP Chi-restraints excluded: chain J residue 108 CYS Chi-restraints excluded: chain J residue 123 ASP Chi-restraints excluded: chain J residue 138 SER 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: 4.9990 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 157 optimal weight: 0.0040 chunk 65 optimal weight: 1.9990 chunk 161 optimal weight: 0.0370 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 0.5070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN D 99 ASN E 99 ASN F 76 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 86 HIS ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN K 99 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.178850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134388 restraints weight = 19107.200| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.42 r_work: 0.3276 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16214 Z= 0.145 Angle : 0.494 12.535 21791 Z= 0.262 Chirality : 0.044 0.167 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.479 12.940 2255 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.02 % Allowed : 22.46 % 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: 1.19 (0.19), residues: 2002 helix: 1.72 (0.18), residues: 792 sheet: 0.87 (0.24), residues: 484 loop : -0.25 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 84 HIS 0.002 0.001 HIS A 86 PHE 0.008 0.001 PHE G 110 TYR 0.029 0.001 TYR C 171 ARG 0.003 0.000 ARG E 46 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3510.60 seconds wall clock time: 64 minutes 36.08 seconds (3876.08 seconds total)