Starting phenix.real_space_refine (version: 1.21rc1) on Sun Apr 23 21:46:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/04_2023/8h1p_34430.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/04_2023/8h1p_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_34430/04_2023/8h1p_34430.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/04_2023/8h1p_34430.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/04_2023/8h1p_34430.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h1p_34430/04_2023/8h1p_34430.pdb" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 8.77, per 1000 atoms: 0.55 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: 5.71 Conformation dependent library (CDL) restraints added in 2.4 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: 0.66 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: 4.07 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5434 1.34 - 1.46: 2510 1.46 - 1.57: 8160 1.57 - 1.69: 0 1.69 - 1.81: 110 Bond restraints: 16214 Sorted by residual: bond pdb=" CB ASN I 100 " pdb=" CG ASN I 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.39e+00 bond pdb=" CB ASN C 100 " pdb=" CG ASN C 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.38e+00 bond pdb=" CB ASN H 100 " pdb=" CG ASN H 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.35e+00 bond pdb=" CB ASN E 100 " pdb=" CG ASN E 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.34e+00 bond pdb=" CB ASN G 100 " pdb=" CG ASN G 100 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.34e+00 ... (remaining 16209 not shown) Histogram of bond angle deviations from ideal: 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: 0.440 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: 3.200 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 40.100 Find NCS groups from input model: 1.100 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: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.330 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.282 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.2653 time to fit residues: 165.0790 Evaluate side-chains 281 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6877 ------------------------------------------------------------------------------- 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: 0.7980 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: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** A 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 73 ASN ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS E 99 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 121 HIS H 164 ASN I 30 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 16214 Z= 0.204 Angle : 0.501 6.044 21791 Z= 0.271 Chirality : 0.044 0.261 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.611 13.358 2255 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.91 % 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: 0.90 (0.18), residues: 2002 helix: 1.11 (0.17), residues: 770 sheet: 0.83 (0.25), residues: 484 loop : 0.05 (0.21), residues: 748 *********************** 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 401 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 352 time to evaluate : 1.849 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 19 residues processed: 377 average time/residue: 0.2470 time to fit residues: 142.7796 Evaluate side-chains 323 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 304 time to evaluate : 1.975 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1467 time to fit residues: 7.9838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 99 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 180 optimal weight: 7.9990 chunk 194 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 178 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 144 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 B 30 GLN B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 ASN D 99 ASN ** D 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 30 GLN G 37 GLN ** G 45 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 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 HIS ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 16214 Z= 0.266 Angle : 0.520 6.955 21791 Z= 0.282 Chirality : 0.044 0.178 2299 Planarity : 0.003 0.023 2882 Dihedral : 3.708 16.560 2255 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.18), residues: 2002 helix: 1.22 (0.18), residues: 781 sheet: 0.95 (0.24), residues: 484 loop : -0.25 (0.21), residues: 737 *********************** 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 384 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 352 time to evaluate : 2.009 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 16 residues processed: 373 average time/residue: 0.2436 time to fit residues: 140.4687 Evaluate side-chains 323 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 307 time to evaluate : 1.967 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1458 time to fit residues: 7.2239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 93 optimal weight: 0.0770 chunk 19 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 180 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 171 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 overall best weight: 0.7742 ------------------------------------------------------------------------------- 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 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 73 ASN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** C 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 30 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN E 121 HIS F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 37 GLN G 45 GLN G 91 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 ASN ** 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 76 ASN ** J 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 99 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 16214 Z= 0.155 Angle : 0.463 11.975 21791 Z= 0.249 Chirality : 0.042 0.194 2299 Planarity : 0.002 0.022 2882 Dihedral : 3.539 14.769 2255 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer Outliers : 1.96 % 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: 1.18 (0.18), residues: 2002 helix: 1.52 (0.18), residues: 781 sheet: 1.15 (0.25), residues: 473 loop : -0.19 (0.21), residues: 748 *********************** 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 385 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 352 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 8 residues processed: 372 average time/residue: 0.2356 time to fit residues: 137.0909 Evaluate side-chains 311 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 303 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1403 time to fit residues: 4.7083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 8.9990 chunk 108 optimal weight: 9.9990 chunk 2 optimal weight: 0.4980 chunk 142 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 0.0270 chunk 171 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 1.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 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** B 176 ASN C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN D 121 HIS E 30 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 ASN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 16214 Z= 0.217 Angle : 0.504 11.737 21791 Z= 0.272 Chirality : 0.044 0.233 2299 Planarity : 0.003 0.022 2882 Dihedral : 3.632 14.926 2255 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2002 helix: 1.66 (0.18), residues: 770 sheet: 0.93 (0.24), residues: 484 loop : -0.21 (0.21), residues: 748 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4004 Ramachandran restraints generated. 2002 Oldfield, 0 Emsley, 2002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 329 time to evaluate : 1.836 Fit side-chains outliers start: 20 outliers final: 9 residues processed: 336 average time/residue: 0.2391 time to fit residues: 125.0494 Evaluate side-chains 297 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 288 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1380 time to fit residues: 4.9351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 15 optimal weight: 0.0370 chunk 63 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN ** 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** B 176 ASN C 30 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 92 ASN G 99 ASN ** H 91 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 91 GLN J 99 ASN ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN ** K 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 16214 Z= 0.241 Angle : 0.510 12.368 21791 Z= 0.275 Chirality : 0.044 0.221 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.683 14.227 2255 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.18), residues: 2002 helix: 1.59 (0.18), residues: 770 sheet: 1.52 (0.28), residues: 374 loop : -0.31 (0.20), residues: 858 *********************** 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 357 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 330 time to evaluate : 1.980 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 341 average time/residue: 0.2426 time to fit residues: 128.9268 Evaluate side-chains 298 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 284 time to evaluate : 1.811 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1425 time to fit residues: 6.4837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 92 ASN A 99 ASN B 30 GLN ** B 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN C 30 GLN C 91 GLN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 30 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN ** G 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 ASN H 99 ASN I 30 GLN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN J 30 GLN K 30 GLN K 76 ASN ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN K 99 ASN K 121 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16214 Z= 0.164 Angle : 0.474 12.834 21791 Z= 0.255 Chirality : 0.043 0.154 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.514 13.555 2255 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.19), residues: 2002 helix: 1.66 (0.18), residues: 781 sheet: 0.93 (0.25), residues: 484 loop : -0.23 (0.22), residues: 737 *********************** 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 335 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 323 time to evaluate : 1.900 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 328 average time/residue: 0.2494 time to fit residues: 127.0839 Evaluate side-chains 285 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 279 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1391 time to fit residues: 4.3056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 121 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 99 ASN B 30 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 121 HIS C 164 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 30 GLN G 92 ASN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN K 30 GLN K 99 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 16214 Z= 0.156 Angle : 0.476 12.670 21791 Z= 0.255 Chirality : 0.043 0.165 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.451 13.159 2255 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 2002 helix: 1.65 (0.18), residues: 792 sheet: 0.91 (0.24), residues: 484 loop : -0.29 (0.22), residues: 726 *********************** 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 310 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 300 time to evaluate : 1.749 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 305 average time/residue: 0.2485 time to fit residues: 117.5208 Evaluate side-chains 270 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1437 time to fit residues: 3.8543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 6.9990 chunk 182 optimal weight: 0.0050 chunk 166 optimal weight: 4.9990 chunk 177 optimal weight: 0.0010 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 160 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** C 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 99 ASN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 16214 Z= 0.174 Angle : 0.497 12.925 21791 Z= 0.265 Chirality : 0.044 0.180 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.465 12.877 2255 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.19), residues: 2002 helix: 1.59 (0.18), residues: 792 sheet: 0.89 (0.24), residues: 484 loop : -0.29 (0.22), residues: 726 *********************** 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 300 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 288 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 290 average time/residue: 0.2415 time to fit residues: 110.0020 Evaluate side-chains 268 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 261 time to evaluate : 1.896 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1441 time to fit residues: 4.6974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 89 optimal weight: 0.0870 chunk 130 optimal weight: 0.6980 chunk 197 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 ASN C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 30 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN F 99 ASN G 99 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3519 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= 0.212 Angle : 0.518 12.840 21791 Z= 0.278 Chirality : 0.045 0.176 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.582 12.512 2255 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 2002 helix: 1.57 (0.18), residues: 781 sheet: 0.88 (0.24), residues: 484 loop : -0.20 (0.22), residues: 737 ********************** 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 283 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 279 time to evaluate : 1.903 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 282 average time/residue: 0.2520 time to fit residues: 110.2034 Evaluate side-chains 263 residues out of total 1683 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 2.334 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1435 time to fit residues: 3.2738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 138 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 ASN B 30 GLN ** B 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 99 ASN ** C 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 GLN C 99 ASN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 ASN ** E 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 76 ASN ** H 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 GLN K 99 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.174317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.129713 restraints weight = 19122.417| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.48 r_work: 0.3271 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 16214 Z= 0.165 Angle : 0.502 12.751 21791 Z= 0.268 Chirality : 0.044 0.222 2299 Planarity : 0.003 0.021 2882 Dihedral : 3.501 12.122 2255 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 0.30 % 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: 1.20 (0.19), residues: 2002 helix: 1.67 (0.18), residues: 781 sheet: 0.93 (0.24), residues: 484 loop : -0.15 (0.22), residues: 737 =============================================================================== Job complete usr+sys time: 3235.45 seconds wall clock time: 59 minutes 43.06 seconds (3583.06 seconds total)