Starting phenix.real_space_refine on Thu Jan 18 19:06:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6x_25730/01_2024/7t6x_25730.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6x_25730/01_2024/7t6x_25730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6x_25730/01_2024/7t6x_25730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6x_25730/01_2024/7t6x_25730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6x_25730/01_2024/7t6x_25730.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t6x_25730/01_2024/7t6x_25730.pdb" } resolution = 3.83 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= 0.025 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 55 5.16 5 C 5783 2.51 5 N 1540 2.21 5 O 1839 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U GLU 655": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 10": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 9217 Number of models: 1 Model: "" Number of chains: 19 Chain: "U" Number of atoms: 2336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2336 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 25, 'TRANS': 272} Chain: "H" Number of atoms: 1093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1093 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 8, 'TRANS': 131} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 802 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "A" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 960 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "B" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 785 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98} Chain: "C" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1059 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 9, 'TRANS': 134} Chain: "E" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 915 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 10, 'TRANS': 107} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.35, per 1000 atoms: 0.58 Number of scatterers: 9217 At special positions: 0 Unit cell: (127.65, 117.3, 105.8, 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 55 16.00 O 1839 8.00 N 1540 7.00 C 5783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS U 429 " - pdb=" SG CYS U 503 " distance=2.02 Simple disulfide: pdb=" SG CYS U 452 " - pdb=" SG CYS U 620 " distance=2.05 Simple disulfide: pdb=" SG CYS U 459 " - pdb=" SG CYS U 486 " distance=2.02 Simple disulfide: pdb=" SG CYS U 494 " - pdb=" SG CYS U 564 " distance=2.03 Simple disulfide: pdb=" SG CYS U 508 " - pdb=" SG CYS U 552 " distance=2.03 Simple disulfide: pdb=" SG CYS U 569 " - pdb=" SG CYS U 597 " distance=2.02 Simple disulfide: pdb=" SG CYS U 581 " - pdb=" SG CYS U 585 " distance=2.02 Simple disulfide: pdb=" SG CYS U 607 " - pdb=" SG CYS U 644 " distance=2.03 Simple disulfide: pdb=" SG CYS U 652 " - pdb=" SG CYS U 677 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.02 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS C 100d" - pdb=" SG CYS C 100i" distance=2.03 Simple disulfide: pdb=" SG CYS E 207 " - pdb=" SG CYS E 226 " distance=2.02 Simple disulfide: pdb=" SG CYS E 229 " - pdb=" SG CYS E 304 " distance=2.02 Simple disulfide: pdb=" SG CYS E 238 " - pdb=" SG CYS E 306 " distance=2.06 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 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " ALPHA1-6 " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG E 401 " - " ASN E 234 " " NAG F 1 " - " ASN U 448 " " NAG G 1 " - " ASN U 540 " " NAG I 1 " - " ASN U 556 " " NAG J 1 " - " ASN U 623 " " NAG K 1 " - " ASN U 645 " " NAG M 1 " - " ASN U 695 " " NAG N 1 " - " ASN E 305 " " NAG O 1 " - " ASN E 196 " " NAG P 1 " - " ASN E 209 " " NAG U 801 " - " ASN U 423 " " NAG U 802 " - " ASN U 430 " " NAG U 803 " - " ASN U 476 " " NAG U 804 " - " ASN U 532 " " NAG U 805 " - " ASN U 576 " Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.8 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 28 sheets defined 9.6% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'U' and resid 421 through 425 Processing helix chain 'U' and resid 438 through 443 removed outlier: 3.826A pdb=" N ILE U 442 " --> pdb=" O ILE U 438 " (cutoff:3.500A) Processing helix chain 'U' and resid 451 through 456 Processing helix chain 'U' and resid 457 through 459 No H-bonds generated for 'chain 'U' and resid 457 through 459' Processing helix chain 'U' and resid 461 through 465 Processing helix chain 'U' and resid 500 through 502 No H-bonds generated for 'chain 'U' and resid 500 through 502' Processing helix chain 'U' and resid 593 through 598 Processing helix chain 'U' and resid 613 through 618 Processing helix chain 'U' and resid 653 through 657 Processing helix chain 'U' and resid 711 through 715 Processing helix chain 'H' and resid 100E through 100I Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'A' and resid 61 through 64 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'B' and resid 50 through 54 Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'C' and resid 52h through 52l Sorry: Error in SS definitions, most likely atoms are absent for one of them.