Starting phenix.real_space_refine (version: dev) on Mon Dec 12 04:13:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2022/8azs_15770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2022/8azs_15770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2022/8azs_15770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2022/8azs_15770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2022/8azs_15770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2022/8azs_15770.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 11": "OE1" <-> "OE2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F ASP 23": "OD1" <-> "OD2" Residue "G TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 11": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 23": "OD1" <-> "OD2" Residue "I TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 11": "OE1" <-> "OE2" Residue "I GLU 22": "OE1" <-> "OE2" Residue "I ASP 23": "OD1" <-> "OD2" Residue "J TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 11": "OE1" <-> "OE2" Residue "J GLU 22": "OE1" <-> "OE2" Residue "J ASP 23": "OD1" <-> "OD2" Residue "K TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 11": "OE1" <-> "OE2" Residue "K GLU 22": "OE1" <-> "OE2" Residue "K ASP 23": "OD1" <-> "OD2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 11": "OE1" <-> "OE2" Residue "L GLU 22": "OE1" <-> "OE2" Residue "L ASP 23": "OD1" <-> "OD2" Residue "M TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 11": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M ASP 23": "OD1" <-> "OD2" Residue "N TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 11": "OE1" <-> "OE2" Residue "N GLU 22": "OE1" <-> "OE2" Residue "N ASP 23": "OD1" <-> "OD2" Residue "O TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 11": "OE1" <-> "OE2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O ASP 23": "OD1" <-> "OD2" Residue "P TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 11": "OE1" <-> "OE2" Residue "P GLU 22": "OE1" <-> "OE2" Residue "P ASP 23": "OD1" <-> "OD2" Residue "Q TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 11": "OE1" <-> "OE2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q ASP 23": "OD1" <-> "OD2" Residue "R TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 11": "OE1" <-> "OE2" Residue "R GLU 22": "OE1" <-> "OE2" Residue "R ASP 23": "OD1" <-> "OD2" Residue "H TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 11": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 11": "OE1" <-> "OE2" Residue "E GLU 22": "OE1" <-> "OE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "S TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 11": "OE1" <-> "OE2" Residue "S GLU 22": "OE1" <-> "OE2" Residue "S ASP 23": "OD1" <-> "OD2" Residue "T TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 11": "OE1" <-> "OE2" Residue "T GLU 22": "OE1" <-> "OE2" Residue "T ASP 23": "OD1" <-> "OD2" Residue "U TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 11": "OE1" <-> "OE2" Residue "U GLU 22": "OE1" <-> "OE2" Residue "U ASP 23": "OD1" <-> "OD2" Residue "V TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 11": "OE1" <-> "OE2" Residue "V GLU 22": "OE1" <-> "OE2" Residue "V ASP 23": "OD1" <-> "OD2" Residue "W TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 11": "OE1" <-> "OE2" Residue "W GLU 22": "OE1" <-> "OE2" Residue "W ASP 23": "OD1" <-> "OD2" Residue "X TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 11": "OE1" <-> "OE2" Residue "X GLU 22": "OE1" <-> "OE2" Residue "X ASP 23": "OD1" <-> "OD2" Residue "Y TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 11": "OE1" <-> "OE2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y ASP 23": "OD1" <-> "OD2" Residue "Z TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 11": "OE1" <-> "OE2" Residue "Z GLU 22": "OE1" <-> "OE2" Residue "Z ASP 23": "OD1" <-> "OD2" Residue "0 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 11": "OE1" <-> "OE2" Residue "0 GLU 22": "OE1" <-> "OE2" Residue "0 ASP 23": "OD1" <-> "OD2" Residue "1 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 GLU 11": "OE1" <-> "OE2" Residue "1 GLU 22": "OE1" <-> "OE2" Residue "1 ASP 23": "OD1" <-> "OD2" Residue "2 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 11": "OE1" <-> "OE2" Residue "2 GLU 22": "OE1" <-> "OE2" Residue "2 ASP 23": "OD1" <-> "OD2" Residue "3 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 11": "OE1" <-> "OE2" Residue "3 GLU 22": "OE1" <-> "OE2" Residue "3 ASP 23": "OD1" <-> "OD2" Residue "4 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 11": "OE1" <-> "OE2" Residue "4 GLU 22": "OE1" <-> "OE2" Residue "4 ASP 23": "OD1" <-> "OD2" Residue "5 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 GLU 11": "OE1" <-> "OE2" Residue "5 GLU 22": "OE1" <-> "OE2" Residue "5 ASP 23": "OD1" <-> "OD2" Residue "6 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 11": "OE1" <-> "OE2" Residue "6 GLU 22": "OE1" <-> "OE2" Residue "6 ASP 23": "OD1" <-> "OD2" Residue "7 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 11": "OE1" <-> "OE2" Residue "7 GLU 22": "OE1" <-> "OE2" Residue "7 ASP 23": "OD1" <-> "OD2" Residue "8 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 11": "OE1" <-> "OE2" Residue "8 GLU 22": "OE1" <-> "OE2" Residue "8 ASP 23": "OD1" <-> "OD2" Residue "9 TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 GLU 11": "OE1" <-> "OE2" Residue "9 GLU 22": "OE1" <-> "OE2" Residue "9 ASP 23": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "I" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "J" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "L" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "M" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "N" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "P" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "Q" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "R" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "H" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "E" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "S" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "T" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "U" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "V" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "W" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "X" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "Y" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "Z" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "0" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "1" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "2" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "3" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "4" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "5" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "6" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "7" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "8" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Chain: "9" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 251 Classifications: {'peptide': 34} Modifications used: {'COO': 1} Link IDs: {'TRANS': 33} Time building chain proxies: 5.24, per 1000 atoms: 0.58 Number of scatterers: 9036 At special positions: 0 Unit cell: (73.959, 63.987, 45.705, 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 36 16.00 O 1620 8.00 N 1512 7.00 C 5868 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: 24.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 24.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2250 1.33 - 1.45: 2150 1.45 - 1.57: 4708 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9180 Sorted by residual: bond pdb=" CE1 HIS G 13 " pdb=" NE2 HIS G 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" CE1 HIS N 13 " pdb=" NE2 HIS N 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" CE1 HIS 6 13 " pdb=" NE2 HIS 6 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 bond pdb=" CE1 HIS 0 13 " pdb=" NE2 HIS 0 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 bond pdb=" CE1 HIS O 13 " pdb=" NE2 HIS O 13 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.91e+01 ... (remaining 9175 not shown) Histogram of bond angle deviations from ideal: 99.98 - 105.72: 36 105.72 - 111.47: 3642 111.47 - 117.21: 2910 117.21 - 122.96: 4552 122.96 - 128.70: 1208 Bond angle restraints: 12348 Sorted by residual: angle pdb=" C GLN 5 15 " pdb=" CA GLN 5 15 " pdb=" CB GLN 5 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN Z 15 " pdb=" CA GLN Z 15 " pdb=" CB GLN Z 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN K 15 " pdb=" CA GLN K 15 " pdb=" CB GLN K 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN Q 15 " pdb=" CA GLN Q 15 " pdb=" CB GLN Q 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.22e+01 angle pdb=" C GLN N 15 " pdb=" CA GLN N 15 " pdb=" CB GLN N 15 " ideal model delta sigma weight residual 109.53 115.42 -5.89 1.69e+00 3.50e-01 1.21e+01 ... (remaining 12343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 4644 17.38 - 34.75: 288 34.75 - 52.13: 144 52.13 - 69.51: 0 69.51 - 86.89: 36 Dihedral angle restraints: 5112 sinusoidal: 1872 harmonic: 3240 Sorted by residual: dihedral pdb=" CA VAL T 36 " pdb=" C VAL T 36 " pdb=" N GLY T 37 " pdb=" CA GLY T 37 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL A 36 " pdb=" C VAL A 36 " pdb=" N GLY A 37 " pdb=" CA GLY A 37 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA VAL U 36 " pdb=" C VAL U 36 " pdb=" N GLY U 37 " pdb=" CA GLY U 37 " ideal model delta harmonic sigma weight residual -180.00 -161.81 -18.19 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 246 0.047 - 0.093: 438 0.093 - 0.139: 352 0.139 - 0.186: 296 0.186 - 0.232: 72 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CB ILE W 31 " pdb=" CA ILE W 31 " pdb=" CG1 ILE W 31 " pdb=" CG2 ILE W 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE D 31 " pdb=" CA ILE D 31 " pdb=" CG1 ILE D 31 " pdb=" CG2 ILE D 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE I 31 " pdb=" CA ILE I 31 " pdb=" CG1 ILE I 31 " pdb=" CG2 ILE I 31 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1401 not shown) Planarity restraints: 1584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS 3 14 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C HIS 3 14 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS 3 14 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN 3 15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS 9 14 " -0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C HIS 9 14 " 0.041 2.00e-02 2.50e+03 pdb=" O HIS 9 14 " -0.015 2.00e-02 2.50e+03 pdb=" N GLN 9 15 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 14 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.66e+00 pdb=" C HIS A 14 " -0.041 2.00e-02 2.50e+03 pdb=" O HIS A 14 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 15 " 0.014 2.00e-02 2.50e+03 ... (remaining 1581 not shown) Histogram of nonbonded interaction distances: 0.02 - 0.99: 5996 0.99 - 1.97: 19210 1.97 - 2.95: 66994 2.95 - 3.92: 129816 3.92 - 4.90: 183014 Warning: very small nonbonded interaction distances. Nonbonded interactions: 405030 Sorted by model distance: nonbonded pdb=" CD1 LEU S 34 " pdb=" CD1 LEU 5 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU K 34 " pdb=" CD1 LEU H 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU H 34 " pdb=" CD1 LEU Z 34 " model vdw 0.017 3.880 nonbonded pdb=" CD1 LEU Q 34 " pdb=" CD1 LEU S 34 " model vdw 0.017 3.880 nonbonded pdb=" CD2 LEU L 34 " pdb=" CD2 LEU C 34 " model vdw 0.017 3.880 ... (remaining 405025 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 '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = 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' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5868 2.51 5 N 1512 2.21 5 O 1620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 4.290 Check model and map are aligned: 0.150 Convert atoms to be neutral: 0.090 Process input model: 58.470 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4012 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 : 0.011 0.072 9180 Z= 0.768 Angle : 1.502 7.059 12348 Z= 0.989 Chirality : 0.115 0.232 1404 Planarity : 0.008 0.024 1584 Dihedral : 16.095 86.885 3096 Min Nonbonded Distance : 0.017 Molprobity Statistics. All-atom Clashscore : 1346.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.21), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.16), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 1.009 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.3645 time to fit residues: 238.1853 Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 30.0000 chunk 81 optimal weight: 40.0000 chunk 45 optimal weight: 30.0000 chunk 27 optimal weight: 0.0060 chunk 55 optimal weight: 50.0000 chunk 43 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 51 optimal weight: 50.0000 chunk 63 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 overall best weight: 14.0012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 HIS ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2051 moved from start: 7.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.079 0.778 9180 Z= 4.251 Angle : 7.694 66.673 12348 Z= 4.647 Chirality : 0.499 4.598 1404 Planarity : 0.034 0.118 1584 Dihedral : 25.995 96.532 1260 Min Nonbonded Distance : 1.355 Molprobity Statistics. All-atom Clashscore : 917.48 Ramachandran Plot: Outliers : 26.04 % Allowed : 34.20 % Favored : 39.76 % Rotamer Outliers : 36.11 % Cbeta Deviations : 32.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 20.88 % 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: -8.29 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.31 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 116 time to evaluate : 0.942 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: 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: 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: 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 outliers start: 325 outliers final: 186 residues processed: 394 average time/residue: 0.5763 time to fit residues: 260.3271 Evaluate side-chains 291 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 105 time to evaluate : 0.966 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 186 outliers final: 157 residues processed: 32 average time/residue: 0.6337 time to fit residues: 24.1288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 50.0000 chunk 30 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 78 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 HIS K 14 HIS ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 HIS M 13 HIS ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 HIS ** Q 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS ** Q 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 13 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1729 moved from start: 7.9013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.049 0.634 9180 Z= 2.588 Angle : 5.592 54.401 12348 Z= 3.284 Chirality : 0.339 4.035 1404 Planarity : 0.026 0.095 1584 Dihedral : 23.715 88.203 1260 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 658.22 Ramachandran Plot: Outliers : 17.45 % Allowed : 39.32 % Favored : 43.23 % Rotamer Outliers : 38.89 % Cbeta Deviations : 14.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.70 % 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: -8.26 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.29 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 125 time to evaluate : 0.962 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 350 outliers final: 208 residues processed: 418 average time/residue: 0.6189 time to fit residues: 293.6062 Evaluate side-chains 314 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 106 time to evaluate : 0.947 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 208 outliers final: 177 residues processed: 33 average time/residue: 0.6103 time to fit residues: 24.0051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 98 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 93 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1804 moved from start: 8.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.040 0.457 9180 Z= 2.042 Angle : 4.814 58.177 12348 Z= 2.776 Chirality : 0.266 3.935 1404 Planarity : 0.022 0.094 1584 Dihedral : 22.990 84.703 1260 Min Nonbonded Distance : 1.574 Molprobity Statistics. All-atom Clashscore : 547.08 Ramachandran Plot: Outliers : 12.41 % Allowed : 45.31 % Favored : 42.27 % Rotamer Outliers : 35.44 % Cbeta Deviations : 7.44 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.18 % 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: -8.22 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.26 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 111 time to evaluate : 1.066 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: 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: 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 outliers start: 319 outliers final: 179 residues processed: 382 average time/residue: 0.5339 time to fit residues: 235.7431 Evaluate side-chains 277 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 98 time to evaluate : 0.902 Switching outliers to nearest non-outliers outliers start: 179 outliers final: 155 residues processed: 27 average time/residue: 0.5821 time to fit residues: 18.9905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 14 HIS ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 13 HIS Q 14 HIS ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1763 moved from start: 8.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.035 0.435 9180 Z= 1.765 Angle : 4.366 54.278 12348 Z= 2.499 Chirality : 0.227 2.441 1404 Planarity : 0.020 0.113 1584 Dihedral : 23.422 84.188 1260 Min Nonbonded Distance : 1.700 Molprobity Statistics. All-atom Clashscore : 479.90 Ramachandran Plot: Outliers : 10.33 % Allowed : 47.40 % Favored : 42.27 % Rotamer Outliers : 31.33 % Cbeta Deviations : 4.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.69 % 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: -8.36 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.36 (0.08), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 115 time to evaluate : 0.972 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 282 outliers final: 167 residues processed: 357 average time/residue: 0.5559 time to fit residues: 229.6803 Evaluate side-chains 270 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 103 time to evaluate : 0.912 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 167 outliers final: 145 residues processed: 24 average time/residue: 0.4235 time to fit residues: 13.3654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 20.0000 chunk 54 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1880 moved from start: 8.7074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.032 0.321 9180 Z= 1.579 Angle : 4.050 44.103 12348 Z= 2.309 Chirality : 0.200 1.885 1404 Planarity : 0.019 0.087 1584 Dihedral : 23.618 89.850 1260 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 433.68 Ramachandran Plot: Outliers : 8.59 % Allowed : 46.61 % Favored : 44.79 % Rotamer Outliers : 30.56 % Cbeta Deviations : 2.78 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.11 % 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: -8.19 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.24 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 110 time to evaluate : 0.997 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 275 outliers final: 165 residues processed: 352 average time/residue: 0.5746 time to fit residues: 231.4625 Evaluate side-chains 264 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 99 time to evaluate : 0.987 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 165 outliers final: 145 residues processed: 21 average time/residue: 0.7964 time to fit residues: 19.7678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 59 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 87 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 48 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 13 HIS ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1903 moved from start: 8.8545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.029 0.308 9180 Z= 1.442 Angle : 3.935 47.210 12348 Z= 2.194 Chirality : 0.199 1.877 1404 Planarity : 0.018 0.073 1584 Dihedral : 23.398 89.807 1260 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 402.14 Ramachandran Plot: Outliers : 8.33 % Allowed : 46.44 % Favored : 45.23 % Rotamer Outliers : 26.67 % Cbeta Deviations : 3.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.95 % 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: -8.15 (0.12), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.21 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 98 time to evaluate : 1.014 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: 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: 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: symmetry clash outliers start: 240 outliers final: 153 residues processed: 315 average time/residue: 0.5741 time to fit residues: 206.9252 Evaluate side-chains 241 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 88 time to evaluate : 0.885 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 153 outliers final: 136 residues processed: 18 average time/residue: 0.6187 time to fit residues: 13.6692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 13 HIS ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 13 HIS ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1825 moved from start: 8.9833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.028 0.281 9180 Z= 1.347 Angle : 3.754 42.840 12348 Z= 2.076 Chirality : 0.202 2.095 1404 Planarity : 0.017 0.064 1584 Dihedral : 23.314 83.696 1260 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 371.77 Ramachandran Plot: Outliers : 7.99 % Allowed : 47.66 % Favored : 44.36 % Rotamer Outliers : 23.89 % Cbeta Deviations : 2.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 19.53 % 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: -8.14 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.20 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 91 time to evaluate : 0.921 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: 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: 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 outliers start: 215 outliers final: 155 residues processed: 275 average time/residue: 0.6216 time to fit residues: 193.7516 Evaluate side-chains 241 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 86 time to evaluate : 0.866 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 155 outliers final: 133 residues processed: 24 average time/residue: 0.6319 time to fit residues: 18.3799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 27 ASN ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1824 moved from start: 9.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.027 0.273 9180 Z= 1.287 Angle : 3.636 47.695 12348 Z= 2.004 Chirality : 0.199 2.046 1404 Planarity : 0.016 0.063 1584 Dihedral : 23.004 87.262 1260 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 355.37 Ramachandran Plot: Outliers : 6.94 % Allowed : 49.57 % Favored : 43.49 % Rotamer Outliers : 21.89 % Cbeta Deviations : 2.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.86 % 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: -8.15 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.21 (0.09), residues: 1152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 86 time to evaluate : 1.025 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 197 outliers final: 143 residues processed: 258 average time/residue: 0.5884 time to fit residues: 173.4935 Evaluate side-chains 225 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 82 time to evaluate : 0.984 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 143 outliers final: 124 residues processed: 20 average time/residue: 0.8217 time to fit residues: 19.3200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1646 moved from start: 9.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.026 0.274 9180 Z= 1.263 Angle : 3.654 48.342 12348 Z= 1.986 Chirality : 0.193 1.622 1404 Planarity : 0.016 0.062 1584 Dihedral : 22.943 85.822 1260 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 343.94 Ramachandran Plot: Outliers : 6.86 % Allowed : 50.35 % Favored : 42.80 % Rotamer Outliers : 19.00 % Cbeta Deviations : 1.79 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.52 % 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: -8.16 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.21 (0.09), residues: 1152 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2304 Ramachandran restraints generated. 1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 74 time to evaluate : 0.967 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: 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 outliers start: 171 outliers final: 139 residues processed: 222 average time/residue: 0.6242 time to fit residues: 158.6936 Evaluate side-chains 212 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 73 time to evaluate : 1.007 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 139 outliers final: 122 residues processed: 18 average time/residue: 0.7881 time to fit residues: 17.0685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.6704 r_free = 0.6704 target = 0.534392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.6686 r_free = 0.6686 target = 0.502689 restraints weight = 9794.740| |-----------------------------------------------------------------------------| r_work (start): 0.6642 rms_B_bonded: 2.19 r_work: 0.6666 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.6526 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.6526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2163 moved from start: 9.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.027 0.285 9180 Z= 1.271 Angle : 3.674 52.876 12348 Z= 1.994 Chirality : 0.194 1.421 1404 Planarity : 0.016 0.060 1584 Dihedral : 22.919 84.079 1260 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 345.70 Ramachandran Plot: Outliers : 5.90 % Allowed : 51.74 % Favored : 42.36 % Rotamer Outliers : 17.67 % Cbeta Deviations : 2.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 18.69 % 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: -8.21 (0.11), residues: 1152 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -6.25 (0.09), residues: 1152 =============================================================================== Job complete usr+sys time: 7391.35 seconds wall clock time: 134 minutes 9.95 seconds (8049.95 seconds total)