Starting phenix.real_space_refine on Mon Mar 18 11:20:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/03_2024/8gi2_40060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/03_2024/8gi2_40060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/03_2024/8gi2_40060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/03_2024/8gi2_40060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/03_2024/8gi2_40060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gi2_40060/03_2024/8gi2_40060.pdb" } resolution = 3.0 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= 0.003 sd= 0.124 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 60 5.16 5 C 12780 2.51 5 N 3400 2.21 5 O 4580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 64": "OE1" <-> "OE2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 163": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 163": "OD1" <-> "OD2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 163": "OD1" <-> "OD2" Residue "E GLU 64": "OE1" <-> "OE2" Residue "E TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 163": "OD1" <-> "OD2" Residue "F GLU 64": "OE1" <-> "OE2" Residue "F TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 163": "OD1" <-> "OD2" Residue "H GLU 64": "OE1" <-> "OE2" Residue "H TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 163": "OD1" <-> "OD2" Residue "I GLU 64": "OE1" <-> "OE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 163": "OD1" <-> "OD2" Residue "J GLU 64": "OE1" <-> "OE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 163": "OD1" <-> "OD2" Residue "K GLU 64": "OE1" <-> "OE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 163": "OD1" <-> "OD2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 163": "OD1" <-> "OD2" Residue "M GLU 64": "OE1" <-> "OE2" Residue "M TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 163": "OD1" <-> "OD2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 163": "OD1" <-> "OD2" Residue "O GLU 64": "OE1" <-> "OE2" Residue "O TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 163": "OD1" <-> "OD2" Residue "P GLU 64": "OE1" <-> "OE2" Residue "P TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 163": "OD1" <-> "OD2" Residue "Q GLU 64": "OE1" <-> "OE2" Residue "Q TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 163": "OD1" <-> "OD2" Residue "R GLU 64": "OE1" <-> "OE2" Residue "R TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 163": "OD1" <-> "OD2" Residue "S GLU 64": "OE1" <-> "OE2" Residue "S TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 163": "OD1" <-> "OD2" Residue "T GLU 64": "OE1" <-> "OE2" Residue "T TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 163": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20820 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "B" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "C" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "D" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "E" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "F" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "G" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "H" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "I" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "K" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "L" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "M" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "N" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "O" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "P" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "Q" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "R" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "S" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "T" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1041 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 144} Time building chain proxies: 11.23, per 1000 atoms: 0.54 Number of scatterers: 20820 At special positions: 0 Unit cell: (117.72, 117.72, 197.64, 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 60 16.00 O 4580 8.00 N 3400 7.00 C 12780 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: 8.10 Conformation dependent library (CDL) restraints added in 4.1 seconds 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5200 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 40 sheets defined 19.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'A' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL A 25 " --> pdb=" O PRO A 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE A 34 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL B 25 " --> pdb=" O PRO B 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL C 25 " --> pdb=" O PRO C 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE C 34 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL D 25 " --> pdb=" O PRO D 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL E 25 " --> pdb=" O PRO E 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE E 34 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL F 25 " --> pdb=" O PRO F 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE F 34 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL G 25 " --> pdb=" O PRO G 21 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL H 25 " --> pdb=" O PRO H 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE H 34 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL I 25 " --> pdb=" O PRO I 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE I 34 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP I 45 " --> pdb=" O ALA I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL J 25 " --> pdb=" O PRO J 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE J 34 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP J 45 " --> pdb=" O ALA J 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL K 25 " --> pdb=" O PRO K 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE K 34 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP K 45 " --> pdb=" O ALA K 41 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL L 25 " --> pdb=" O PRO L 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP L 45 " --> pdb=" O ALA L 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL M 25 " --> pdb=" O PRO M 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE M 34 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL N 25 " --> pdb=" O PRO N 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE N 34 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL O 25 " --> pdb=" O PRO O 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE O 34 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP O 45 " --> pdb=" O ALA O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL P 25 " --> pdb=" O PRO P 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE P 34 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL Q 25 " --> pdb=" O PRO Q 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE Q 34 " --> pdb=" O ALA Q 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 19 through 46 removed outlier: 3.629A pdb=" N VAL R 25 " --> pdb=" O PRO R 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL S 25 " --> pdb=" O PRO S 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE S 34 " --> pdb=" O ALA S 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 46 removed outlier: 3.630A pdb=" N VAL T 25 " --> pdb=" O PRO T 21 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE T 34 " --> pdb=" O ALA T 30 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 58 through 63 Processing sheet with id= 2, first strand: chain 'A' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA A 140 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN A 150 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE A 142 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG A 148 " --> pdb=" O ILE A 142 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 58 through 63 Processing sheet with id= 4, first strand: chain 'B' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA B 140 " --> pdb=" O GLN B 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN B 150 " --> pdb=" O ALA B 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE B 142 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG B 148 " --> pdb=" O ILE B 142 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 58 through 63 Processing sheet with id= 6, first strand: chain 'C' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA C 140 " --> pdb=" O GLN C 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN C 150 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE C 142 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG C 148 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 58 through 63 Processing sheet with id= 8, first strand: chain 'D' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA D 140 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN D 150 " --> pdb=" O ALA D 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE D 142 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG D 148 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'E' and resid 58 through 63 Processing sheet with id= 10, first strand: chain 'E' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA E 140 " --> pdb=" O GLN E 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN E 150 " --> pdb=" O ALA E 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE E 142 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG E 148 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 58 through 63 Processing sheet with id= 12, first strand: chain 'F' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA F 140 " --> pdb=" O GLN F 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN F 150 " --> pdb=" O ALA F 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE F 142 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG F 148 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 58 through 63 Processing sheet with id= 14, first strand: chain 'G' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA G 140 " --> pdb=" O GLN G 150 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N GLN G 150 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE G 142 " --> pdb=" O ARG G 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG G 148 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'H' and resid 58 through 63 Processing sheet with id= 16, first strand: chain 'H' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA H 140 " --> pdb=" O GLN H 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN H 150 " --> pdb=" O ALA H 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE H 142 " --> pdb=" O ARG H 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG H 148 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'I' and resid 58 through 63 Processing sheet with id= 18, first strand: chain 'I' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA I 140 " --> pdb=" O GLN I 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN I 150 " --> pdb=" O ALA I 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE I 142 " --> pdb=" O ARG I 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG I 148 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'J' and resid 58 through 63 Processing sheet with id= 20, first strand: chain 'J' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA J 140 " --> pdb=" O GLN J 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN J 150 " --> pdb=" O ALA J 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE J 142 " --> pdb=" O ARG J 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG J 148 " --> pdb=" O ILE J 142 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'K' and resid 58 through 63 Processing sheet with id= 22, first strand: chain 'K' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA K 140 " --> pdb=" O GLN K 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN K 150 " --> pdb=" O ALA K 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE K 142 " --> pdb=" O ARG K 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG K 148 " --> pdb=" O ILE K 142 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 58 through 63 Processing sheet with id= 24, first strand: chain 'L' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA L 140 " --> pdb=" O GLN L 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN L 150 " --> pdb=" O ALA L 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE L 142 " --> pdb=" O ARG L 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG L 148 " --> pdb=" O ILE L 142 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 58 through 63 Processing sheet with id= 26, first strand: chain 'M' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA M 140 " --> pdb=" O GLN M 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN M 150 " --> pdb=" O ALA M 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE M 142 " --> pdb=" O ARG M 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG M 148 " --> pdb=" O ILE M 142 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 58 through 63 Processing sheet with id= 28, first strand: chain 'N' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA N 140 " --> pdb=" O GLN N 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN N 150 " --> pdb=" O ALA N 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE N 142 " --> pdb=" O ARG N 148 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ARG N 148 " --> pdb=" O ILE N 142 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 58 through 63 Processing sheet with id= 30, first strand: chain 'O' and resid 82 through 87 removed outlier: 6.280A pdb=" N ALA O 140 " --> pdb=" O GLN O 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN O 150 " --> pdb=" O ALA O 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE O 142 " --> pdb=" O ARG O 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG O 148 " --> pdb=" O ILE O 142 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 58 through 63 Processing sheet with id= 32, first strand: chain 'P' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA P 140 " --> pdb=" O GLN P 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN P 150 " --> pdb=" O ALA P 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE P 142 " --> pdb=" O ARG P 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG P 148 " --> pdb=" O ILE P 142 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 58 through 63 Processing sheet with id= 34, first strand: chain 'Q' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA Q 140 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN Q 150 " --> pdb=" O ALA Q 140 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE Q 142 " --> pdb=" O ARG Q 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG Q 148 " --> pdb=" O ILE Q 142 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 58 through 63 Processing sheet with id= 36, first strand: chain 'R' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA R 140 " --> pdb=" O GLN R 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN R 150 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE R 142 " --> pdb=" O ARG R 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG R 148 " --> pdb=" O ILE R 142 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 58 through 63 Processing sheet with id= 38, first strand: chain 'S' and resid 82 through 87 removed outlier: 6.279A pdb=" N ALA S 140 " --> pdb=" O GLN S 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN S 150 " --> pdb=" O ALA S 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE S 142 " --> pdb=" O ARG S 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG S 148 " --> pdb=" O ILE S 142 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 58 through 63 Processing sheet with id= 40, first strand: chain 'T' and resid 82 through 87 removed outlier: 6.278A pdb=" N ALA T 140 " --> pdb=" O GLN T 150 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN T 150 " --> pdb=" O ALA T 140 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE T 142 " --> pdb=" O ARG T 148 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ARG T 148 " --> pdb=" O ILE T 142 " (cutoff:3.500A) 860 hydrogen bonds defined for protein. 2340 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.49 Time building geometry restraints manager: 8.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4140 1.32 - 1.44: 4500 1.44 - 1.56: 12200 1.56 - 1.68: 0 1.68 - 1.80: 120 Bond restraints: 20960 Sorted by residual: bond pdb=" CA TYR F 127 " pdb=" CB TYR F 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.51e+01 bond pdb=" CA TYR I 127 " pdb=" CB TYR I 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.51e+01 bond pdb=" CA TYR O 127 " pdb=" CB TYR O 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 bond pdb=" CA TYR G 127 " pdb=" CB TYR G 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 bond pdb=" CA TYR J 127 " pdb=" CB TYR J 127 " ideal model delta sigma weight residual 1.530 1.454 0.076 1.51e-02 4.39e+03 2.50e+01 ... (remaining 20955 not shown) Histogram of bond angle deviations from ideal: 100.35 - 106.53: 460 106.53 - 112.70: 11460 112.70 - 118.88: 5920 118.88 - 125.06: 10640 125.06 - 131.23: 100 Bond angle restraints: 28580 Sorted by residual: angle pdb=" N TYR T 127 " pdb=" CA TYR T 127 " pdb=" C TYR T 127 " ideal model delta sigma weight residual 112.93 106.41 6.52 1.12e+00 7.97e-01 3.39e+01 angle pdb=" N TYR J 127 " pdb=" CA TYR J 127 " pdb=" C TYR J 127 " ideal model delta sigma weight residual 112.93 106.42 6.51 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR E 127 " pdb=" CA TYR E 127 " pdb=" C TYR E 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR O 127 " pdb=" CA TYR O 127 " pdb=" C TYR O 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.37e+01 angle pdb=" N TYR M 127 " pdb=" CA TYR M 127 " pdb=" C TYR M 127 " ideal model delta sigma weight residual 112.93 106.43 6.50 1.12e+00 7.97e-01 3.36e+01 ... (remaining 28575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.62: 11317 12.62 - 25.24: 763 25.24 - 37.85: 220 37.85 - 50.47: 80 50.47 - 63.09: 60 Dihedral angle restraints: 12440 sinusoidal: 4260 harmonic: 8180 Sorted by residual: dihedral pdb=" N SER T 131 " pdb=" C SER T 131 " pdb=" CA SER T 131 " pdb=" CB SER T 131 " ideal model delta harmonic sigma weight residual 122.80 114.19 8.61 0 2.50e+00 1.60e-01 1.19e+01 dihedral pdb=" N SER K 131 " pdb=" C SER K 131 " pdb=" CA SER K 131 " pdb=" CB SER K 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" N SER S 131 " pdb=" C SER S 131 " pdb=" CA SER S 131 " pdb=" CB SER S 131 " ideal model delta harmonic sigma weight residual 122.80 114.20 8.60 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 12437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2202 0.038 - 0.076: 937 0.076 - 0.114: 362 0.114 - 0.152: 119 0.152 - 0.190: 40 Chirality restraints: 3660 Sorted by residual: chirality pdb=" CA SER Q 130 " pdb=" N SER Q 130 " pdb=" C SER Q 130 " pdb=" CB SER Q 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.06e-01 chirality pdb=" CA SER R 130 " pdb=" N SER R 130 " pdb=" C SER R 130 " pdb=" CB SER R 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA SER B 130 " pdb=" N SER B 130 " pdb=" C SER B 130 " pdb=" CB SER B 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 ... (remaining 3657 not shown) Planarity restraints: 3760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN Q 117 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.38e+01 pdb=" C ASN Q 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN Q 117 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA Q 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN N 117 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN N 117 " -0.064 2.00e-02 2.50e+03 pdb=" O ASN N 117 " 0.025 2.00e-02 2.50e+03 pdb=" N ALA N 118 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 117 " -0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ASN M 117 " 0.064 2.00e-02 2.50e+03 pdb=" O ASN M 117 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA M 118 " -0.021 2.00e-02 2.50e+03 ... (remaining 3757 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 29 2.18 - 2.86: 8122 2.86 - 3.54: 27384 3.54 - 4.22: 47857 4.22 - 4.90: 83245 Nonbonded interactions: 166637 Sorted by model distance: nonbonded pdb=" OE2 GLU M 146 " pdb=" OE1 GLU T 64 " model vdw 1.504 3.040 nonbonded pdb=" OE2 GLU F 146 " pdb=" OE1 GLU L 64 " model vdw 1.505 3.040 nonbonded pdb=" OE2 GLU I 146 " pdb=" OE1 GLU O 64 " model vdw 1.505 3.040 nonbonded pdb=" OE2 GLU C 146 " pdb=" OE1 GLU J 64 " model vdw 1.505 3.040 nonbonded pdb=" OE1 GLU A 64 " pdb=" OE2 GLU E 146 " model vdw 1.505 3.040 ... (remaining 166632 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' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } 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=0.00 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: 0.820 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: 4.880 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.590 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.150 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:11.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.008 0.076 20960 Z= 0.504 Angle : 0.975 7.771 28580 Z= 0.613 Chirality : 0.052 0.190 3660 Planarity : 0.004 0.037 3760 Dihedral : 11.484 63.089 7240 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 31.63 Ramachandran Plot: Outliers : 0.69 % Allowed : 12.97 % Favored : 86.34 % Rotamer: Outliers : 3.45 % Allowed : 4.31 % Favored : 92.24 % 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: -3.41 (0.14), residues: 2900 helix: -1.19 (0.24), residues: 560 sheet: -0.76 (0.17), residues: 940 loop : -3.96 (0.10), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 82 PHE 0.003 0.001 PHE P 159 TYR 0.007 0.001 TYR H 127 ARG 0.001 0.000 ARG J 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 646 time to evaluate : 2.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8090 (mt-10) REVERT: A 127 TYR cc_start: 0.6109 (OUTLIER) cc_final: 0.5314 (t80) REVERT: C 127 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.4616 (t80) REVERT: D 127 TYR cc_start: 0.6130 (OUTLIER) cc_final: 0.4625 (t80) REVERT: E 124 VAL cc_start: 0.5185 (OUTLIER) cc_final: 0.4607 (p) REVERT: F 124 VAL cc_start: 0.4596 (OUTLIER) cc_final: 0.4235 (p) REVERT: F 143 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7979 (mt-10) REVERT: G 96 TYR cc_start: 0.6763 (t80) cc_final: 0.6061 (t80) REVERT: G 127 TYR cc_start: 0.6532 (OUTLIER) cc_final: 0.5026 (t80) REVERT: H 63 ASP cc_start: 0.8019 (t0) cc_final: 0.7777 (t0) REVERT: H 96 TYR cc_start: 0.6884 (t80) cc_final: 0.6599 (t80) REVERT: H 112 ASP cc_start: 0.7874 (m-30) cc_final: 0.7495 (m-30) REVERT: H 127 TYR cc_start: 0.6473 (OUTLIER) cc_final: 0.5030 (t80) REVERT: J 63 ASP cc_start: 0.8323 (t0) cc_final: 0.8081 (t0) REVERT: J 73 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8032 (mt-10) REVERT: K 96 TYR cc_start: 0.7253 (t80) cc_final: 0.7021 (t80) REVERT: K 127 TYR cc_start: 0.6151 (OUTLIER) cc_final: 0.4957 (t80) REVERT: M 28 MET cc_start: 0.8702 (mmt) cc_final: 0.8447 (mmt) REVERT: M 73 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8076 (mt-10) REVERT: M 96 TYR cc_start: 0.7146 (t80) cc_final: 0.6869 (t80) REVERT: M 127 TYR cc_start: 0.5940 (OUTLIER) cc_final: 0.5358 (t80) REVERT: N 63 ASP cc_start: 0.7739 (t0) cc_final: 0.7380 (t70) REVERT: N 127 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5196 (t80) REVERT: O 127 TYR cc_start: 0.5923 (OUTLIER) cc_final: 0.5266 (t80) REVERT: P 129 LEU cc_start: 0.6516 (mt) cc_final: 0.6263 (mt) REVERT: R 127 TYR cc_start: 0.6191 (OUTLIER) cc_final: 0.4805 (t80) REVERT: R 129 LEU cc_start: 0.6056 (mt) cc_final: 0.5738 (mt) REVERT: S 94 THR cc_start: 0.6564 (t) cc_final: 0.6323 (m) REVERT: S 127 TYR cc_start: 0.6009 (OUTLIER) cc_final: 0.4818 (t80) REVERT: T 127 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.4276 (t80) outliers start: 80 outliers final: 44 residues processed: 706 average time/residue: 0.9970 time to fit residues: 819.2772 Evaluate side-chains 626 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 568 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain D residue 131 SER Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain G residue 119 ASN Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 131 SER Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 131 SER Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain O residue 131 SER Chi-restraints excluded: chain P residue 119 ASN Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 119 ASN Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 131 SER Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 131 SER Chi-restraints excluded: chain S residue 64 GLU Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 131 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 133 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 254 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN D 117 ASN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 117 ASN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 126 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN L 55 GLN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 ASN M 82 HIS M 117 ASN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 126 ASN N 117 ASN ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 ASN ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 126 ASN ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 ASN S 117 ASN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20960 Z= 0.180 Angle : 0.626 13.175 28580 Z= 0.316 Chirality : 0.047 0.148 3660 Planarity : 0.003 0.021 3760 Dihedral : 6.972 78.666 3120 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 7.03 % Allowed : 14.31 % Favored : 78.66 % 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: -2.48 (0.15), residues: 2900 helix: 0.37 (0.23), residues: 560 sheet: -0.25 (0.18), residues: 960 loop : -3.74 (0.11), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 82 PHE 0.018 0.002 PHE T 42 TYR 0.008 0.001 TYR F 127 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 568 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8418 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 81 ASP cc_start: 0.7976 (m-30) cc_final: 0.7731 (m-30) REVERT: C 127 TYR cc_start: 0.6031 (OUTLIER) cc_final: 0.4693 (t80) REVERT: D 31 ILE cc_start: 0.9003 (mt) cc_final: 0.8690 (mp) REVERT: F 64 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: F 143 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8003 (mt-10) REVERT: H 63 ASP cc_start: 0.8122 (t0) cc_final: 0.7869 (t0) REVERT: H 112 ASP cc_start: 0.7944 (m-30) cc_final: 0.7475 (m-30) REVERT: I 44 LEU cc_start: 0.8906 (mt) cc_final: 0.8679 (mt) REVERT: I 90 ASP cc_start: 0.6567 (t0) cc_final: 0.6259 (t0) REVERT: J 44 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8639 (mt) REVERT: J 63 ASP cc_start: 0.8355 (t0) cc_final: 0.8152 (t0) REVERT: J 73 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8028 (mt-10) REVERT: J 119 ASN cc_start: 0.8052 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: K 96 TYR cc_start: 0.7305 (t80) cc_final: 0.6895 (t80) REVERT: K 127 TYR cc_start: 0.5765 (OUTLIER) cc_final: 0.4952 (t80) REVERT: M 73 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8107 (mt-10) REVERT: M 108 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8792 (mt) REVERT: M 148 ARG cc_start: 0.8169 (mtp85) cc_final: 0.7903 (mtm180) REVERT: N 81 ASP cc_start: 0.8010 (m-30) cc_final: 0.7618 (m-30) REVERT: N 96 TYR cc_start: 0.7579 (t80) cc_final: 0.7121 (t80) REVERT: N 127 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4872 (t80) REVERT: O 96 TYR cc_start: 0.7490 (t80) cc_final: 0.6744 (t80) REVERT: O 127 TYR cc_start: 0.5822 (OUTLIER) cc_final: 0.4795 (t80) REVERT: R 127 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.4505 (t80) REVERT: S 94 THR cc_start: 0.6670 (t) cc_final: 0.6431 (m) REVERT: S 119 ASN cc_start: 0.8116 (OUTLIER) cc_final: 0.7767 (m-40) REVERT: S 127 TYR cc_start: 0.5856 (OUTLIER) cc_final: 0.4840 (t80) outliers start: 163 outliers final: 83 residues processed: 638 average time/residue: 1.1778 time to fit residues: 856.5309 Evaluate side-chains 622 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 528 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain J residue 19 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 123 SER Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 90 ASP Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain R residue 46 LEU Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 108 LEU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain T residue 23 ILE Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 173 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 chunk 275 optimal weight: 0.4980 chunk 226 optimal weight: 2.9990 chunk 252 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 204 optimal weight: 0.0040 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 117 ASN ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 93 GLN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 ASN ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 ASN ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20960 Z= 0.137 Angle : 0.601 15.079 28580 Z= 0.293 Chirality : 0.046 0.147 3660 Planarity : 0.002 0.021 3760 Dihedral : 6.286 83.458 3082 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 6.38 % Allowed : 15.95 % Favored : 77.67 % 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: -1.82 (0.15), residues: 2900 helix: 0.89 (0.23), residues: 560 sheet: 0.34 (0.18), residues: 940 loop : -3.42 (0.11), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 82 PHE 0.014 0.001 PHE T 42 TYR 0.006 0.001 TYR F 127 ARG 0.000 0.000 ARG P 148 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 554 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8894 (mp) REVERT: A 73 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 81 ASP cc_start: 0.7981 (m-30) cc_final: 0.7683 (m-30) REVERT: A 127 TYR cc_start: 0.5410 (OUTLIER) cc_final: 0.4906 (t80) REVERT: A 143 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7844 (mt-10) REVERT: C 127 TYR cc_start: 0.6042 (OUTLIER) cc_final: 0.5166 (t80) REVERT: D 31 ILE cc_start: 0.8962 (mt) cc_final: 0.8671 (mp) REVERT: D 127 TYR cc_start: 0.5823 (OUTLIER) cc_final: 0.4789 (t80) REVERT: E 26 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8644 (mm) REVERT: H 63 ASP cc_start: 0.7903 (t0) cc_final: 0.7687 (t0) REVERT: J 44 LEU cc_start: 0.8713 (mp) cc_final: 0.8481 (mt) REVERT: J 73 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8024 (mt-10) REVERT: J 119 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: K 96 TYR cc_start: 0.7194 (t80) cc_final: 0.6573 (t80) REVERT: K 127 TYR cc_start: 0.5740 (OUTLIER) cc_final: 0.5038 (t80) REVERT: L 90 ASP cc_start: 0.6451 (t0) cc_final: 0.6250 (t0) REVERT: M 73 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8145 (mt-10) REVERT: M 108 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8787 (mt) REVERT: N 81 ASP cc_start: 0.7975 (m-30) cc_final: 0.7636 (m-30) REVERT: N 96 TYR cc_start: 0.7404 (t80) cc_final: 0.6715 (t80) REVERT: N 127 TYR cc_start: 0.5502 (OUTLIER) cc_final: 0.4955 (t80) REVERT: O 31 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8825 (mp) REVERT: O 127 TYR cc_start: 0.5734 (OUTLIER) cc_final: 0.4799 (t80) REVERT: P 143 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8081 (mt-10) REVERT: R 127 TYR cc_start: 0.5879 (OUTLIER) cc_final: 0.4712 (t80) REVERT: S 96 TYR cc_start: 0.7346 (t80) cc_final: 0.7055 (t80) REVERT: S 119 ASN cc_start: 0.8080 (OUTLIER) cc_final: 0.7773 (m-40) REVERT: S 127 TYR cc_start: 0.5864 (OUTLIER) cc_final: 0.5030 (t80) REVERT: S 133 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7402 (mp0) outliers start: 148 outliers final: 64 residues processed: 610 average time/residue: 1.1929 time to fit residues: 829.1719 Evaluate side-chains 603 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 524 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 93 GLN Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 45 ASP Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 123 SER Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 121 optimal weight: 6.9990 chunk 171 optimal weight: 4.9990 chunk 255 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 133 optimal weight: 0.0060 chunk 242 optimal weight: 0.0050 chunk 72 optimal weight: 1.9990 overall best weight: 0.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN E 117 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 117 ASN ** J 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 117 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 ASN ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 ASN R 117 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20960 Z= 0.147 Angle : 0.612 18.662 28580 Z= 0.290 Chirality : 0.046 0.147 3660 Planarity : 0.002 0.023 3760 Dihedral : 5.864 53.849 3074 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.11 % Allowed : 17.24 % Favored : 75.65 % 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: -1.50 (0.15), residues: 2900 helix: 1.24 (0.23), residues: 560 sheet: 0.32 (0.19), residues: 960 loop : -3.11 (0.12), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Q 82 PHE 0.011 0.001 PHE T 42 TYR 0.005 0.001 TYR H 127 ARG 0.001 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 529 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8132 (mt-10) REVERT: A 127 TYR cc_start: 0.5356 (OUTLIER) cc_final: 0.4925 (t80) REVERT: A 143 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 103 THR cc_start: 0.6050 (OUTLIER) cc_final: 0.5547 (p) REVERT: D 31 ILE cc_start: 0.8988 (mt) cc_final: 0.8727 (mp) REVERT: D 127 TYR cc_start: 0.5789 (OUTLIER) cc_final: 0.4780 (t80) REVERT: E 26 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8605 (mm) REVERT: F 64 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: H 63 ASP cc_start: 0.7863 (t0) cc_final: 0.7647 (t0) REVERT: J 73 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8064 (mt-10) REVERT: J 119 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7492 (m-40) REVERT: K 96 TYR cc_start: 0.7293 (t80) cc_final: 0.6647 (t80) REVERT: K 127 TYR cc_start: 0.5752 (OUTLIER) cc_final: 0.5055 (t80) REVERT: L 44 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8445 (mp) REVERT: L 126 ASN cc_start: 0.5296 (p0) cc_final: 0.5070 (p0) REVERT: M 73 GLU cc_start: 0.8338 (mt-10) cc_final: 0.8089 (mt-10) REVERT: M 94 THR cc_start: 0.7036 (OUTLIER) cc_final: 0.6806 (m) REVERT: M 108 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8810 (mt) REVERT: N 81 ASP cc_start: 0.8003 (m-30) cc_final: 0.7634 (m-30) REVERT: N 96 TYR cc_start: 0.7440 (t80) cc_final: 0.6607 (t80) REVERT: N 127 TYR cc_start: 0.5475 (OUTLIER) cc_final: 0.5009 (t80) REVERT: O 31 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8755 (mp) REVERT: O 55 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7971 (mt0) REVERT: O 96 TYR cc_start: 0.7489 (t80) cc_final: 0.6589 (t80) REVERT: O 127 TYR cc_start: 0.5681 (OUTLIER) cc_final: 0.4858 (t80) REVERT: P 143 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8110 (mt-10) REVERT: R 127 TYR cc_start: 0.5843 (OUTLIER) cc_final: 0.4901 (t80) REVERT: S 133 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7395 (mp0) outliers start: 165 outliers final: 83 residues processed: 602 average time/residue: 1.1511 time to fit residues: 793.5827 Evaluate side-chains 605 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 506 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 90 ASP Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 119 ASN Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 127 TYR Chi-restraints excluded: chain I residue 45 ASP Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 133 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain O residue 31 ILE Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 55 GLN Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 103 THR Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 230 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 242 optimal weight: 0.6980 chunk 68 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 117 ASN C 119 ASN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 120 ASN J 120 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 117 ASN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 ASN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 119 ASN ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20960 Z= 0.226 Angle : 0.657 19.483 28580 Z= 0.311 Chirality : 0.048 0.156 3660 Planarity : 0.002 0.027 3760 Dihedral : 6.084 53.088 3072 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 7.84 % Allowed : 18.32 % Favored : 73.84 % 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: -1.37 (0.15), residues: 2900 helix: 1.25 (0.21), residues: 580 sheet: 0.29 (0.18), residues: 960 loop : -2.95 (0.12), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS O 82 PHE 0.009 0.001 PHE J 42 TYR 0.007 0.001 TYR K 96 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 542 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8868 (mp) REVERT: A 73 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8070 (mt-10) REVERT: A 127 TYR cc_start: 0.5433 (OUTLIER) cc_final: 0.4942 (t80) REVERT: B 103 THR cc_start: 0.6244 (OUTLIER) cc_final: 0.5736 (p) REVERT: C 127 TYR cc_start: 0.6011 (OUTLIER) cc_final: 0.5219 (t80) REVERT: D 31 ILE cc_start: 0.9010 (mt) cc_final: 0.8780 (mp) REVERT: D 162 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7905 (mmmt) REVERT: E 26 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8659 (mm) REVERT: E 93 GLN cc_start: 0.5092 (OUTLIER) cc_final: 0.4120 (pp30) REVERT: F 64 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: F 90 ASP cc_start: 0.6688 (t0) cc_final: 0.6430 (t0) REVERT: F 144 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7856 (tt0) REVERT: H 63 ASP cc_start: 0.8039 (t0) cc_final: 0.7818 (t0) REVERT: J 73 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8103 (mt-10) REVERT: J 96 TYR cc_start: 0.7295 (t80) cc_final: 0.5922 (t80) REVERT: J 119 ASN cc_start: 0.8324 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: J 127 TYR cc_start: 0.5857 (OUTLIER) cc_final: 0.5310 (t80) REVERT: K 96 TYR cc_start: 0.7379 (t80) cc_final: 0.6640 (t80) REVERT: K 127 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.5053 (t80) REVERT: L 61 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6684 (pp20) REVERT: L 144 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: M 73 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8117 (mt-10) REVERT: M 94 THR cc_start: 0.7165 (OUTLIER) cc_final: 0.6925 (m) REVERT: M 108 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8836 (mt) REVERT: N 81 ASP cc_start: 0.8059 (m-30) cc_final: 0.7640 (m-30) REVERT: N 127 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.5006 (t80) REVERT: N 143 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7919 (mt-10) REVERT: O 127 TYR cc_start: 0.5606 (OUTLIER) cc_final: 0.4719 (t80) REVERT: P 127 TYR cc_start: 0.5713 (OUTLIER) cc_final: 0.4803 (t80) REVERT: R 127 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4881 (t80) REVERT: S 133 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7447 (mp0) outliers start: 182 outliers final: 93 residues processed: 621 average time/residue: 1.2055 time to fit residues: 851.3227 Evaluate side-chains 637 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 524 time to evaluate : 2.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 127 TYR Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 59 ASN Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 22 VAL Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 127 TYR Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 0.0370 chunk 243 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 66 optimal weight: 0.0970 chunk 270 optimal weight: 1.9990 chunk 224 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 22 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 126 ASN ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 ASN E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 GLN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 126 ASN M 59 ASN ** M 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20960 Z= 0.212 Angle : 0.666 19.450 28580 Z= 0.310 Chirality : 0.048 0.152 3660 Planarity : 0.002 0.027 3760 Dihedral : 6.054 52.710 3072 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 7.37 % Allowed : 19.48 % Favored : 73.15 % 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: -1.28 (0.15), residues: 2900 helix: 1.32 (0.21), residues: 580 sheet: 0.31 (0.18), residues: 960 loop : -2.85 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P 82 PHE 0.006 0.001 PHE P 42 TYR 0.005 0.001 TYR K 96 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 532 time to evaluate : 2.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8885 (mp) REVERT: A 59 ASN cc_start: 0.8669 (t0) cc_final: 0.8352 (t0) REVERT: A 61 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: A 73 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8019 (mt-10) REVERT: A 127 TYR cc_start: 0.5470 (OUTLIER) cc_final: 0.5050 (t80) REVERT: A 144 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: B 103 THR cc_start: 0.6266 (OUTLIER) cc_final: 0.5762 (p) REVERT: C 127 TYR cc_start: 0.5819 (OUTLIER) cc_final: 0.5183 (t80) REVERT: D 31 ILE cc_start: 0.8995 (mt) cc_final: 0.8764 (mp) REVERT: D 162 LYS cc_start: 0.8190 (mtmt) cc_final: 0.7824 (mttt) REVERT: E 26 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8677 (mm) REVERT: F 64 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: F 90 ASP cc_start: 0.6808 (t0) cc_final: 0.6606 (t0) REVERT: H 63 ASP cc_start: 0.8060 (t0) cc_final: 0.7835 (t0) REVERT: J 31 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8520 (mp) REVERT: J 73 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8054 (mt-10) REVERT: J 119 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.7614 (m-40) REVERT: K 96 TYR cc_start: 0.7398 (t80) cc_final: 0.6652 (t80) REVERT: K 127 TYR cc_start: 0.5702 (OUTLIER) cc_final: 0.5387 (t80) REVERT: L 144 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7496 (tt0) REVERT: M 73 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8114 (mt-10) REVERT: M 94 THR cc_start: 0.7170 (OUTLIER) cc_final: 0.6930 (m) REVERT: M 108 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8835 (mt) REVERT: N 26 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8752 (mm) REVERT: N 81 ASP cc_start: 0.8022 (m-30) cc_final: 0.7618 (m-30) REVERT: N 96 TYR cc_start: 0.7259 (t80) cc_final: 0.6615 (t80) REVERT: N 127 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.5007 (t80) REVERT: N 143 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7917 (mt-10) REVERT: O 127 TYR cc_start: 0.5633 (OUTLIER) cc_final: 0.4728 (t80) REVERT: P 53 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7074 (mm-30) REVERT: P 127 TYR cc_start: 0.5607 (OUTLIER) cc_final: 0.4682 (t80) REVERT: S 133 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7454 (mp0) outliers start: 171 outliers final: 94 residues processed: 609 average time/residue: 1.2096 time to fit residues: 837.2197 Evaluate side-chains 631 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 518 time to evaluate : 2.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 144 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain D residue 127 TYR Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain H residue 155 ASP Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 126 ASN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 39 ILE Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 197 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 164 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 ASN C 120 ASN D 82 HIS ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 120 ASN L 55 GLN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 ASN ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 82 HIS ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 93 GLN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20960 Z= 0.327 Angle : 0.739 20.374 28580 Z= 0.345 Chirality : 0.050 0.164 3660 Planarity : 0.003 0.030 3760 Dihedral : 6.390 52.821 3068 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 8.02 % Allowed : 19.48 % Favored : 72.50 % 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: -1.33 (0.15), residues: 2900 helix: 1.24 (0.20), residues: 580 sheet: 0.23 (0.18), residues: 960 loop : -2.82 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS P 82 PHE 0.024 0.002 PHE T 42 TYR 0.007 0.001 TYR F 127 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 542 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8986 (mp) REVERT: A 61 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6893 (mp0) REVERT: A 73 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8042 (mt-10) REVERT: A 127 TYR cc_start: 0.5494 (OUTLIER) cc_final: 0.5016 (t80) REVERT: B 103 THR cc_start: 0.6247 (OUTLIER) cc_final: 0.5758 (p) REVERT: B 144 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8110 (tt0) REVERT: C 103 THR cc_start: 0.5338 (OUTLIER) cc_final: 0.4474 (p) REVERT: C 120 ASN cc_start: 0.6973 (OUTLIER) cc_final: 0.6725 (p0) REVERT: C 127 TYR cc_start: 0.5980 (OUTLIER) cc_final: 0.5247 (t80) REVERT: D 31 ILE cc_start: 0.9050 (mt) cc_final: 0.8766 (mp) REVERT: D 162 LYS cc_start: 0.8303 (mtmt) cc_final: 0.8079 (mmmt) REVERT: E 26 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8713 (mm) REVERT: E 112 ASP cc_start: 0.7835 (m-30) cc_final: 0.7559 (m-30) REVERT: E 119 ASN cc_start: 0.8120 (OUTLIER) cc_final: 0.7812 (m110) REVERT: F 64 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: F 90 ASP cc_start: 0.6951 (t0) cc_final: 0.6723 (t0) REVERT: F 144 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: G 64 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: G 144 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: J 73 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8055 (mt-10) REVERT: J 119 ASN cc_start: 0.8552 (OUTLIER) cc_final: 0.7664 (m-40) REVERT: J 133 GLU cc_start: 0.7893 (pt0) cc_final: 0.7684 (pt0) REVERT: J 144 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7637 (tt0) REVERT: K 127 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.5033 (t80) REVERT: L 61 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6809 (pp20) REVERT: L 144 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7550 (tt0) REVERT: M 73 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8116 (mt-10) REVERT: M 108 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8841 (mt) REVERT: N 26 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8761 (mm) REVERT: N 81 ASP cc_start: 0.8079 (m-30) cc_final: 0.7684 (m-30) REVERT: N 96 TYR cc_start: 0.7422 (t80) cc_final: 0.6866 (t80) REVERT: N 127 TYR cc_start: 0.5541 (OUTLIER) cc_final: 0.4948 (t80) REVERT: N 143 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8032 (mt-10) REVERT: O 127 TYR cc_start: 0.5564 (OUTLIER) cc_final: 0.4761 (t80) REVERT: P 127 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.4602 (t80) outliers start: 186 outliers final: 101 residues processed: 632 average time/residue: 1.2242 time to fit residues: 877.3504 Evaluate side-chains 649 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 524 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 60 MET Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 144 GLU Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 50 VAL Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 90 ASP Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 119 ASN Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 50 VAL Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 26 ILE Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 50 VAL Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 119 ASN Chi-restraints excluded: chain O residue 127 TYR Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain R residue 144 GLU Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 108 LEU Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 123 SER Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 161 optimal weight: 0.1980 chunk 81 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** L 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 126 ASN S 93 GLN ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20960 Z= 0.217 Angle : 0.705 20.837 28580 Z= 0.324 Chirality : 0.048 0.153 3660 Planarity : 0.002 0.028 3760 Dihedral : 6.073 53.530 3066 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 6.81 % Allowed : 20.52 % Favored : 72.67 % 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: -1.33 (0.15), residues: 2900 helix: 1.38 (0.21), residues: 540 sheet: 0.27 (0.18), residues: 960 loop : -2.81 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS Q 82 PHE 0.005 0.001 PHE P 42 TYR 0.006 0.001 TYR H 127 ARG 0.001 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 528 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8938 (mp) REVERT: A 61 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6812 (mp0) REVERT: A 73 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8013 (mt-10) REVERT: B 103 THR cc_start: 0.6246 (OUTLIER) cc_final: 0.5788 (p) REVERT: C 127 TYR cc_start: 0.5844 (OUTLIER) cc_final: 0.5193 (t80) REVERT: D 31 ILE cc_start: 0.8999 (mt) cc_final: 0.8761 (mp) REVERT: D 116 ILE cc_start: 0.8753 (mt) cc_final: 0.8530 (mt) REVERT: D 162 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8113 (mmmt) REVERT: E 26 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8688 (mm) REVERT: E 90 ASP cc_start: 0.5933 (t0) cc_final: 0.5702 (p0) REVERT: E 112 ASP cc_start: 0.7797 (m-30) cc_final: 0.7512 (m-30) REVERT: E 119 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7823 (m110) REVERT: F 64 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: F 90 ASP cc_start: 0.6848 (t0) cc_final: 0.6588 (t0) REVERT: F 144 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: G 64 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7961 (mt-10) REVERT: J 31 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8519 (mp) REVERT: J 73 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7958 (mt-10) REVERT: J 119 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.7572 (m-40) REVERT: K 92 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5443 (m-30) REVERT: K 127 TYR cc_start: 0.5670 (OUTLIER) cc_final: 0.5326 (t80) REVERT: L 60 MET cc_start: 0.8739 (mtm) cc_final: 0.8051 (mtm) REVERT: L 61 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6757 (pp20) REVERT: L 144 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: M 73 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8105 (mt-10) REVERT: M 94 THR cc_start: 0.7136 (OUTLIER) cc_final: 0.6839 (m) REVERT: M 108 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8859 (mt) REVERT: N 81 ASP cc_start: 0.8023 (m-30) cc_final: 0.7617 (m-30) REVERT: N 96 TYR cc_start: 0.7361 (t80) cc_final: 0.6544 (t80) REVERT: N 127 TYR cc_start: 0.5535 (OUTLIER) cc_final: 0.5001 (t80) REVERT: N 143 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7952 (mt-10) REVERT: P 107 LYS cc_start: 0.8642 (mptt) cc_final: 0.8322 (mttm) REVERT: P 127 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.4484 (t80) REVERT: R 117 ASN cc_start: 0.8210 (t0) cc_final: 0.7812 (t0) REVERT: S 90 ASP cc_start: 0.5876 (t0) cc_final: 0.5550 (t0) REVERT: S 133 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: T 42 PHE cc_start: 0.9223 (t80) cc_final: 0.8908 (t80) outliers start: 158 outliers final: 92 residues processed: 610 average time/residue: 1.2123 time to fit residues: 840.2714 Evaluate side-chains 630 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 518 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 77 MET Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain H residue 45 ASP Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 60 MET Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 127 TYR Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 127 TYR Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 133 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 8.9990 chunk 258 optimal weight: 10.0000 chunk 235 optimal weight: 3.9990 chunk 251 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 197 optimal weight: 7.9990 chunk 77 optimal weight: 0.0770 chunk 227 optimal weight: 10.0000 chunk 237 optimal weight: 1.9990 chunk 250 optimal weight: 4.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN L 120 ASN M 59 ASN ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 119 ASN ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 GLN P 69 ASN ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 120 ASN ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20960 Z= 0.348 Angle : 0.782 23.171 28580 Z= 0.359 Chirality : 0.051 0.167 3660 Planarity : 0.003 0.029 3760 Dihedral : 6.382 53.698 3062 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 6.68 % Allowed : 20.69 % Favored : 72.63 % 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: -1.38 (0.15), residues: 2900 helix: 1.15 (0.20), residues: 580 sheet: 0.20 (0.18), residues: 960 loop : -2.83 (0.13), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS P 82 PHE 0.007 0.002 PHE S 159 TYR 0.008 0.001 TYR F 127 ARG 0.002 0.000 ARG B 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 535 time to evaluate : 2.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9252 (OUTLIER) cc_final: 0.8989 (mp) REVERT: A 61 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 73 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8034 (mt-10) REVERT: B 103 THR cc_start: 0.6353 (OUTLIER) cc_final: 0.5882 (p) REVERT: C 103 THR cc_start: 0.5235 (OUTLIER) cc_final: 0.4034 (p) REVERT: C 105 LYS cc_start: 0.5089 (pmtt) cc_final: 0.4734 (pmtt) REVERT: C 127 TYR cc_start: 0.6014 (OUTLIER) cc_final: 0.5260 (t80) REVERT: D 31 ILE cc_start: 0.9048 (mt) cc_final: 0.8764 (mp) REVERT: D 116 ILE cc_start: 0.8720 (mt) cc_final: 0.8472 (mt) REVERT: D 162 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8134 (mmmt) REVERT: E 26 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8738 (mm) REVERT: E 90 ASP cc_start: 0.6117 (t0) cc_final: 0.5775 (p0) REVERT: E 112 ASP cc_start: 0.7846 (m-30) cc_final: 0.7570 (m-30) REVERT: E 119 ASN cc_start: 0.8263 (OUTLIER) cc_final: 0.7906 (m110) REVERT: F 64 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: F 90 ASP cc_start: 0.6713 (t0) cc_final: 0.6508 (t0) REVERT: F 144 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7864 (tt0) REVERT: G 64 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7951 (mt-10) REVERT: G 144 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: I 77 MET cc_start: 0.8689 (mmm) cc_final: 0.8487 (mmp) REVERT: I 133 GLU cc_start: 0.7683 (pt0) cc_final: 0.7377 (pt0) REVERT: J 73 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8042 (mt-10) REVERT: J 119 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.7485 (m-40) REVERT: J 144 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7636 (tt0) REVERT: K 92 ASP cc_start: 0.6191 (OUTLIER) cc_final: 0.5575 (m-30) REVERT: K 127 TYR cc_start: 0.5847 (OUTLIER) cc_final: 0.5054 (t80) REVERT: L 60 MET cc_start: 0.8885 (OUTLIER) cc_final: 0.8341 (mtm) REVERT: L 61 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: L 144 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7526 (tt0) REVERT: M 73 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8150 (mt-10) REVERT: M 108 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8820 (mt) REVERT: N 81 ASP cc_start: 0.8100 (m-30) cc_final: 0.7706 (m-30) REVERT: N 143 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8088 (mt-10) REVERT: O 77 MET cc_start: 0.8720 (mmm) cc_final: 0.8508 (tpt) REVERT: P 107 LYS cc_start: 0.8656 (mptt) cc_final: 0.8327 (mttm) REVERT: T 42 PHE cc_start: 0.9253 (t80) cc_final: 0.8934 (t80) outliers start: 155 outliers final: 94 residues processed: 612 average time/residue: 1.2292 time to fit residues: 852.8924 Evaluate side-chains 634 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 521 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 127 TYR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain G residue 144 GLU Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 127 TYR Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 106 LEU Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 60 MET Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 92 ASP Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 127 TYR Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 144 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 256 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20960 Z= 0.279 Angle : 0.768 25.485 28580 Z= 0.350 Chirality : 0.050 0.182 3660 Planarity : 0.003 0.028 3760 Dihedral : 6.117 54.040 3058 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 5.34 % Allowed : 22.16 % Favored : 72.50 % 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: -1.42 (0.15), residues: 2900 helix: 1.28 (0.20), residues: 540 sheet: 0.21 (0.18), residues: 960 loop : -2.84 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 82 PHE 0.007 0.001 PHE J 42 TYR 0.007 0.001 TYR H 127 ARG 0.002 0.000 ARG B 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5800 Ramachandran restraints generated. 2900 Oldfield, 0 Emsley, 2900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 532 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.8981 (mp) REVERT: A 61 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 73 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8014 (mt-10) REVERT: A 143 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 103 THR cc_start: 0.6245 (OUTLIER) cc_final: 0.5835 (p) REVERT: C 96 TYR cc_start: 0.6979 (t80) cc_final: 0.6589 (t80) REVERT: C 103 THR cc_start: 0.5241 (OUTLIER) cc_final: 0.4106 (p) REVERT: C 105 LYS cc_start: 0.5196 (pmtt) cc_final: 0.4895 (pmtt) REVERT: C 127 TYR cc_start: 0.6026 (OUTLIER) cc_final: 0.5301 (t80) REVERT: D 31 ILE cc_start: 0.9045 (mt) cc_final: 0.8762 (mp) REVERT: D 116 ILE cc_start: 0.8707 (mt) cc_final: 0.8467 (mt) REVERT: D 162 LYS cc_start: 0.8384 (mtmt) cc_final: 0.8154 (mmmt) REVERT: E 26 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8717 (mm) REVERT: E 90 ASP cc_start: 0.6109 (t0) cc_final: 0.5805 (p0) REVERT: E 112 ASP cc_start: 0.7822 (m-30) cc_final: 0.7542 (m-30) REVERT: E 119 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7920 (m110) REVERT: F 64 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8229 (mt-10) REVERT: F 90 ASP cc_start: 0.6800 (t0) cc_final: 0.6576 (t0) REVERT: F 144 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7804 (tt0) REVERT: G 64 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7944 (mt-10) REVERT: I 133 GLU cc_start: 0.7682 (pt0) cc_final: 0.7375 (pt0) REVERT: J 31 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8538 (mp) REVERT: J 73 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7990 (mt-10) REVERT: J 119 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.7465 (m-40) REVERT: J 144 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: K 92 ASP cc_start: 0.6656 (OUTLIER) cc_final: 0.6211 (m-30) REVERT: K 127 TYR cc_start: 0.5815 (OUTLIER) cc_final: 0.5001 (t80) REVERT: L 61 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6790 (pp20) REVERT: L 144 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: M 73 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8146 (mt-10) REVERT: M 108 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8798 (mt) REVERT: N 81 ASP cc_start: 0.8024 (m-30) cc_final: 0.7584 (m-30) REVERT: N 143 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8087 (mt-10) REVERT: O 77 MET cc_start: 0.8693 (mmm) cc_final: 0.8472 (tpt) REVERT: P 107 LYS cc_start: 0.8634 (mptt) cc_final: 0.8313 (mttm) REVERT: P 127 TYR cc_start: 0.5796 (m-80) cc_final: 0.4656 (t80) REVERT: T 42 PHE cc_start: 0.9234 (t80) cc_final: 0.8925 (t80) outliers start: 124 outliers final: 89 residues processed: 591 average time/residue: 1.2531 time to fit residues: 838.4472 Evaluate side-chains 630 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 523 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 SER Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 39 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 103 THR Chi-restraints excluded: chain C residue 127 TYR Chi-restraints excluded: chain D residue 45 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 64 GLU Chi-restraints excluded: chain E residue 26 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 106 LEU Chi-restraints excluded: chain E residue 119 ASN Chi-restraints excluded: chain E residue 127 TYR Chi-restraints excluded: chain E residue 145 ASP Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 64 GLU Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain F residue 144 GLU Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 127 TYR Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain H residue 119 ASN Chi-restraints excluded: chain H residue 131 SER Chi-restraints excluded: chain I residue 26 ILE Chi-restraints excluded: chain I residue 59 ASN Chi-restraints excluded: chain I residue 103 THR Chi-restraints excluded: chain I residue 127 TYR Chi-restraints excluded: chain I residue 135 THR Chi-restraints excluded: chain I residue 145 ASP Chi-restraints excluded: chain I residue 154 VAL Chi-restraints excluded: chain J residue 31 ILE Chi-restraints excluded: chain J residue 45 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 144 GLU Chi-restraints excluded: chain J residue 154 VAL Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 45 ASP Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 119 ASN Chi-restraints excluded: chain K residue 127 TYR Chi-restraints excluded: chain K residue 145 ASP Chi-restraints excluded: chain K residue 154 VAL Chi-restraints excluded: chain K residue 155 ASP Chi-restraints excluded: chain L residue 26 ILE Chi-restraints excluded: chain L residue 45 ASP Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 61 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain L residue 119 ASN Chi-restraints excluded: chain L residue 144 GLU Chi-restraints excluded: chain L residue 145 ASP Chi-restraints excluded: chain M residue 19 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 119 ASN Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 127 TYR Chi-restraints excluded: chain M residue 133 GLU Chi-restraints excluded: chain M residue 144 GLU Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 103 THR Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 133 GLU Chi-restraints excluded: chain O residue 50 VAL Chi-restraints excluded: chain O residue 64 GLU Chi-restraints excluded: chain O residue 89 ILE Chi-restraints excluded: chain P residue 50 VAL Chi-restraints excluded: chain P residue 108 LEU Chi-restraints excluded: chain P residue 154 VAL Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 106 LEU Chi-restraints excluded: chain Q residue 116 ILE Chi-restraints excluded: chain Q residue 127 TYR Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 154 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain R residue 61 GLU Chi-restraints excluded: chain R residue 119 ASN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain S residue 45 ASP Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain S residue 119 ASN Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain T residue 50 VAL Chi-restraints excluded: chain T residue 60 MET Chi-restraints excluded: chain T residue 89 ILE Chi-restraints excluded: chain T residue 119 ASN Chi-restraints excluded: chain T residue 127 TYR Chi-restraints excluded: chain T residue 154 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 0.5980 chunk 236 optimal weight: 6.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 222 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 228 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 59 ASN ** E 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 126 ASN ** F 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN ** G 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 GLN M 59 ASN N 117 ASN ** N 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 ASN O 55 GLN ** O 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 GLN ** T 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.147895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121431 restraints weight = 28063.689| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.31 r_work: 0.3260 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 20960 Z= 0.256 Angle : 0.767 27.491 28580 Z= 0.344 Chirality : 0.050 0.171 3660 Planarity : 0.002 0.028 3760 Dihedral : 5.852 54.626 3050 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.34 % Allowed : 22.28 % Favored : 72.37 % 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: -1.40 (0.15), residues: 2900 helix: 1.48 (0.21), residues: 520 sheet: 0.25 (0.18), residues: 960 loop : -2.88 (0.13), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 82 PHE 0.006 0.001 PHE J 42 TYR 0.007 0.001 TYR H 127 ARG 0.001 0.000 ARG B 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11041.72 seconds wall clock time: 193 minutes 39.79 seconds (11619.79 seconds total)