Starting phenix.real_space_refine on Tue Mar 19 02:16:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r93_4767/03_2024/6r93_4767_trim_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.442 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: 6 Type Number sf(0) Gaussians P 324 5.49 5 S 14 5.16 5 C 7072 2.51 5 N 2396 2.21 5 O 3032 1.98 5 H 10123 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A ASP 82": "OD1" <-> "OD2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "D ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 52": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ASP 86": "OD1" <-> "OD2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G ASP 73": "OD1" <-> "OD2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "H ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22961 Number of models: 1 Model: "" Number of chains: 10 Chain: "I" Number of atoms: 5139 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 145, 4594 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Conformer: "B" Number of residues, atoms: 144, 4583 Unusual residues: {'T64': 1} Classifications: {'DNA': 143, 'undetermined': 1} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 141, None: 2} Not linked: pdbres=" DA I 94 " pdbres="T64 I 95 " Not linked: pdbres="T64 I 95 " pdbres=" DG I 97 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 bond proxies already assigned to first conformer: 4352 Chain: "J" Number of atoms: 5142 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 144, 4583 Unusual residues: {'T64': 1} Classifications: {'DNA': 143, 'undetermined': 1} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 141, None: 2} Not linked: pdbres=" DA J 94 " pdbres="T64 J 95 " Not linked: pdbres="T64 J 95 " pdbres=" DG J 97 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Conformer: "B" Number of residues, atoms: 145, 4595 Classifications: {'DNA': 145} Modifications used: {'3*END': 1, '5*END': 1} Link IDs: {'rna3p': 144} bond proxies already assigned to first conformer: 4351 Chain: "A" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1672 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1344 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1784 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1562 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1672 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1350 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 1563 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Residues with excluded nonbonded symmetry interactions: 35 residue: pdb=" P A DC I 47 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B DC I 47 " occ=0.50 residue: pdb=" P A DT I 48 " occ=0.50 ... (62 atoms not shown) pdb=" H6 B DT I 48 " occ=0.50 residue: pdb=" P A DC I 49 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B DC I 49 " occ=0.50 residue group: pdb=" P A DA I 50 " occ=0.50 ... (59 atoms not shown) pdb=" H6 B DC I 50 " occ=0.50 residue: pdb=" P A DA I 51 " occ=0.50 ... (62 atoms not shown) pdb=" H2 B DA I 51 " occ=0.50 residue: pdb=" P A DC I 52 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B DC I 52 " occ=0.50 residue: pdb=" P A DC I 53 " occ=0.50 ... (58 atoms not shown) pdb=" H6 B DC I 53 " occ=0.50 residue: pdb=" P A DA I 54 " occ=0.50 ... (62 atoms not shown) pdb=" H2 B DA I 54 " occ=0.50 residue: pdb=" P A DA I 55 " occ=0.50 ... (62 atoms not shown) pdb=" H2 B DA I 55 " occ=0.50 residue: pdb=" P A DT I 91 " occ=0.50 ... (62 atoms not shown) pdb=" H6 B DT I 91 " occ=0.50 residue: pdb=" P A DT I 92 " occ=0.50 ... (62 atoms not shown) pdb=" H6 B DT I 92 " occ=0.50 residue: pdb=" P A DG I 93 " occ=0.50 ... (64 atoms not shown) pdb=" H22B DG I 93 " occ=0.50 ... (remaining 23 not shown) Time building chain proxies: 13.77, per 1000 atoms: 0.60 Number of scatterers: 22961 At special positions: 0 Unit cell: (122.12, 99.76, 126.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 14 16.00 P 324 15.00 O 3032 8.00 N 2396 7.00 C 7072 6.00 H 10123 1.00 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 Atom "ATOM 3362 O3'B DA I 94 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.09 Conformation dependent library (CDL) restraints added in 1.4 seconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 63.0% alpha, 0.0% beta 144 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 14.25 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 79 removed outlier: 3.582A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'B' and resid 27 through 29 No H-bonds generated for 'chain 'B' and resid 27 through 29' Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 76 Processing helix chain 'B' and resid 84 through 93 Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 48 through 73 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 105 through 124 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.531A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.975A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE F 67 " --> pdb=" O GLU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 93 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 105 through 124 343 hydrogen bonds defined for protein. 963 hydrogen bond angles defined for protein. ('C', 'G') A G 19 A DA I 50 B DG J 96 Sorry: Saenger class does not match residue names