Starting phenix.real_space_refine on Fri Dec 8 18:55:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2023/8azs_15770.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2023/8azs_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_2023/8azs_15770.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2023/8azs_15770.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2023/8azs_15770.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8azs_15770/12_2023/8azs_15770.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.18, per 1000 atoms: 0.57 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: 23.14 Conformation dependent library (CDL) restraints added in 1.7 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: 1.10 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: 22.43 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 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.010 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 58.690 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 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 % Allowed : 8.00 % Favored : 92.00 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.005 HIS P 13 PHE 0.031 0.009 PHE Z 19 TYR 0.017 0.004 TYR I 10 *********************** 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 : 0.903 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: 1.4664 time to fit residues: 255.5805 Evaluate side-chains 153 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 0.944 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.128 > 50: distance: 267 - 268: 17.177 distance: 268 - 269: 5.292 distance: 269 - 270: 11.291 distance: 269 - 271: 3.462 distance: 271 - 272: 19.310 distance: 272 - 273: 4.302 distance: 272 - 275: 8.647 distance: 273 - 274: 5.412 distance: 273 - 283: 12.968 distance: 275 - 276: 10.197 distance: 276 - 277: 9.816 distance: 277 - 279: 4.270 distance: 278 - 280: 7.453 distance: 279 - 281: 4.612 distance: 280 - 281: 6.100 distance: 281 - 282: 13.752 distance: 283 - 284: 3.136 distance: 284 - 285: 16.757 distance: 284 - 287: 15.013 distance: 285 - 286: 5.881 distance: 285 - 292: 5.553 distance: 287 - 288: 20.702 distance: 288 - 289: 20.195 distance: 289 - 290: 28.264 distance: 289 - 291: 24.604 distance: 292 - 293: 18.577 distance: 293 - 294: 11.939 distance: 293 - 296: 15.207 distance: 294 - 295: 23.022 distance: 294 - 299: 13.264 distance: 296 - 297: 11.476 distance: 296 - 298: 13.031 distance: 299 - 300: 17.168 distance: 300 - 301: 5.321 distance: 300 - 303: 11.060 distance: 301 - 302: 12.255 distance: 301 - 309: 15.468 distance: 303 - 304: 10.921 distance: 304 - 305: 11.701 distance: 304 - 306: 14.011 distance: 306 - 308: 12.054 distance: 307 - 308: 12.081 distance: 309 - 310: 18.438 distance: 310 - 311: 6.647 distance: 310 - 313: 6.242 distance: 311 - 312: 16.128 distance: 311 - 319: 8.073 distance: 313 - 314: 11.339 distance: 314 - 315: 6.557 distance: 314 - 316: 17.349 distance: 315 - 317: 7.471 distance: 316 - 318: 10.746 distance: 317 - 318: 11.309 distance: 319 - 320: 12.002 distance: 320 - 321: 11.172 distance: 320 - 323: 6.361 distance: 321 - 322: 17.889 distance: 321 - 328: 4.667 distance: 323 - 324: 10.910 distance: 324 - 325: 6.989 distance: 325 - 326: 8.183 distance: 325 - 327: 4.060 distance: 328 - 329: 15.484 distance: 329 - 330: 15.087 distance: 329 - 332: 10.225 distance: 330 - 331: 24.091 distance: 330 - 337: 23.340 distance: 332 - 333: 18.869 distance: 333 - 334: 3.868 distance: 334 - 335: 38.669 distance: 335 - 336: 36.455 distance: 337 - 338: 27.202 distance: 338 - 339: 19.070 distance: 338 - 341: 38.430 distance: 339 - 340: 15.726 distance: 339 - 345: 3.465 distance: 341 - 342: 22.858 distance: 342 - 343: 23.644 distance: 342 - 344: 8.589