Starting phenix.real_space_refine on Wed Jun 26 06:20:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/06_2024/8blb_16105_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/06_2024/8blb_16105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/06_2024/8blb_16105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/06_2024/8blb_16105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/06_2024/8blb_16105_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blb_16105/06_2024/8blb_16105_updated.pdb" } resolution = 3.3 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= 0.073 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 30 5.16 5 C 6115 2.51 5 N 1515 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 54": "OD1" <-> "OD2" Residue "A ASP 64": "OD1" <-> "OD2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 75": "OE1" <-> "OE2" Residue "A ASP 103": "OD1" <-> "OD2" Residue "A TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B ASP 64": "OD1" <-> "OD2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C ASP 64": "OD1" <-> "OD2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 75": "OE1" <-> "OE2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "C TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D ASP 64": "OD1" <-> "OD2" Residue "D TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E ASP 64": "OD1" <-> "OD2" Residue "E TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 75": "OE1" <-> "OE2" Residue "E ASP 103": "OD1" <-> "OD2" Residue "E TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 224": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9400 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "B" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "C" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "D" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} Chain: "E" Number of atoms: 1789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1789 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 12, 'TRANS': 198} 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: 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" 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: "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: 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: "O" 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: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'VTX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 5.78, per 1000 atoms: 0.61 Number of scatterers: 9400 At special positions: 0 Unit cell: (96.9, 94.62, 79.8, 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 30 16.00 O 1740 8.00 N 1515 7.00 C 6115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A 501 " - " ASN A 104 " " NAG B 501 " - " ASN B 104 " " NAG C 501 " - " ASN C 104 " " NAG D 501 " - " ASN D 104 " " NAG E 501 " - " ASN E 104 " " NAG F 1 " - " ASN A 186 " " NAG G 1 " - " ASN A 170 " " NAG H 1 " - " ASN B 186 " " NAG I 1 " - " ASN B 170 " " NAG J 1 " - " ASN C 186 " " NAG K 1 " - " ASN C 170 " " NAG L 1 " - " ASN D 186 " " NAG M 1 " - " ASN D 170 " " NAG N 1 " - " ASN E 186 " " NAG O 1 " - " ASN E 170 " Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 20 sheets defined 11.4% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 33 through 42 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 164 through 166 No H-bonds generated for 'chain 'A' and resid 164 through 166' Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'B' and resid 33 through 42 Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'C' and resid 33 through 42 Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'D' and resid 33 through 42 Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 164 through 166 No H-bonds generated for 'chain 'D' and resid 164 through 166' Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'E' and resid 33 through 42 Processing helix chain 'E' and resid 99 through 101 No H-bonds generated for 'chain 'E' and resid 99 through 101' Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 164 through 166 No H-bonds generated for 'chain 'E' and resid 164 through 166' Processing helix chain 'E' and resid 193 through 197 Processing sheet with id= A, first strand: chain 'A' and resid 185 through 189 removed outlier: 6.294A pdb=" N THR A 59 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N SER A 188 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 61 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 60 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR A 91 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR A 83 " --> pdb=" O TYR A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 72 through 74 removed outlier: 3.674A pdb=" N ASN A 72 " --> pdb=" O THR A 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 107 through 111 Processing sheet with id= D, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER A 177 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA A 230 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY A 213 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 239 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU A 211 " --> pdb=" O ARG A 239 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 185 through 189 removed outlier: 6.294A pdb=" N THR B 59 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER B 188 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL B 61 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR B 60 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR B 91 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR B 83 " --> pdb=" O TYR B 68 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 72 through 74 removed outlier: 3.674A pdb=" N ASN B 72 " --> pdb=" O THR B 81 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 107 through 111 Processing sheet with id= H, first strand: chain 'B' and resid 120 through 122 removed outlier: 3.871A pdb=" N SER B 177 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA B 230 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY B 213 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG B 239 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU B 211 " --> pdb=" O ARG B 239 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 185 through 189 removed outlier: 6.293A pdb=" N THR C 59 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER C 188 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 61 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR C 60 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR C 91 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR C 83 " --> pdb=" O TYR C 68 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 72 through 74 removed outlier: 3.674A pdb=" N ASN C 72 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 107 through 111 Processing sheet with id= L, first strand: chain 'C' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER C 177 " --> pdb=" O ALA C 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA C 230 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 213 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG C 239 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU C 211 " --> pdb=" O ARG C 239 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.294A pdb=" N THR D 59 " --> pdb=" O ASN D 186 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER D 188 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL D 61 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR D 60 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N THR D 91 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR D 83 " --> pdb=" O TYR D 68 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 72 through 74 removed outlier: 3.674A pdb=" N ASN D 72 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 107 through 111 Processing sheet with id= P, first strand: chain 'D' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER D 177 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ALA D 230 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 213 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ARG D 239 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 211 " --> pdb=" O ARG D 239 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 185 through 189 removed outlier: 6.293A pdb=" N THR E 59 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N SER E 188 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 61 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR E 60 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR E 91 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR E 83 " --> pdb=" O TYR E 68 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 72 through 74 removed outlier: 3.674A pdb=" N ASN E 72 " --> pdb=" O THR E 81 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 107 through 111 Processing sheet with id= T, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.870A pdb=" N SER E 177 " --> pdb=" O ALA E 230 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ALA E 230 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY E 213 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG E 239 " --> pdb=" O LEU E 211 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU E 211 " --> pdb=" O ARG E 239 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2855 1.34 - 1.46: 2599 1.46 - 1.58: 4171 1.58 - 1.70: 0 1.70 - 1.82: 50 Bond restraints: 9675 Sorted by residual: bond pdb=" C12 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 1.404 1.453 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C12 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.85e+00 bond pdb=" C12 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.79e+00 bond pdb=" C12 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 1.404 1.452 -0.048 2.00e-02 2.50e+03 5.70e+00 ... (remaining 9670 not shown) Histogram of bond angle deviations from ideal: 100.57 - 107.25: 394 107.25 - 113.93: 5330 113.93 - 120.62: 3671 120.62 - 127.30: 3665 127.30 - 133.98: 145 Bond angle restraints: 13205 Sorted by residual: angle pdb=" C15 VTX E 502 " pdb=" C14 VTX E 502 " pdb=" N13 VTX E 502 " ideal model delta sigma weight residual 109.33 119.09 -9.76 3.00e+00 1.11e-01 1.06e+01 angle pdb=" C15 VTX D 502 " pdb=" C14 VTX D 502 " pdb=" N13 VTX D 502 " ideal model delta sigma weight residual 109.33 119.06 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX A 502 " pdb=" C14 VTX A 502 " pdb=" N13 VTX A 502 " ideal model delta sigma weight residual 109.33 119.05 -9.72 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX B 502 " pdb=" C14 VTX B 502 " pdb=" N13 VTX B 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C15 VTX C 502 " pdb=" C14 VTX C 502 " pdb=" N13 VTX C 502 " ideal model delta sigma weight residual 109.33 119.04 -9.71 3.00e+00 1.11e-01 1.05e+01 ... (remaining 13200 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.13: 5689 25.13 - 50.25: 316 50.25 - 75.38: 35 75.38 - 100.51: 10 100.51 - 125.63: 5 Dihedral angle restraints: 6055 sinusoidal: 2875 harmonic: 3180 Sorted by residual: dihedral pdb=" C15 VTX A 502 " pdb=" C17 VTX A 502 " pdb=" N16 VTX A 502 " pdb=" C18 VTX A 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.31 -125.63 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX C 502 " pdb=" C17 VTX C 502 " pdb=" N16 VTX C 502 " pdb=" C18 VTX C 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.30 -125.62 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" C15 VTX D 502 " pdb=" C17 VTX D 502 " pdb=" N16 VTX D 502 " pdb=" C18 VTX D 502 " ideal model delta sinusoidal sigma weight residual -69.32 56.29 -125.61 1 3.00e+01 1.11e-03 1.69e+01 ... (remaining 6052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 892 0.029 - 0.057: 348 0.057 - 0.086: 57 0.086 - 0.115: 135 0.115 - 0.143: 58 Chirality restraints: 1490 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 186 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN E 170 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 186 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.07e-01 ... (remaining 1487 not shown) Planarity restraints: 1635 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 98 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.52e+00 pdb=" N PRO C 99 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 98 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.52e+00 pdb=" N PRO E 99 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 99 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 98 " 0.045 5.00e-02 4.00e+02 6.84e-02 7.48e+00 pdb=" N PRO D 99 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " 0.038 5.00e-02 4.00e+02 ... (remaining 1632 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 372 2.72 - 3.26: 8931 3.26 - 3.81: 14760 3.81 - 4.35: 19040 4.35 - 4.90: 33174 Nonbonded interactions: 76277 Sorted by model distance: nonbonded pdb=" OH TYR D 136 " pdb=" O VAL E 117 " model vdw 2.171 2.440 nonbonded pdb=" OH TYR C 136 " pdb=" O VAL D 117 " model vdw 2.233 2.440 nonbonded pdb=" NH2 ARG D 219 " pdb=" OE2 GLU D 231 " model vdw 2.298 2.520 nonbonded pdb=" NH2 ARG A 219 " pdb=" OE2 GLU A 231 " model vdw 2.298 2.520 nonbonded pdb=" NH2 ARG C 219 " pdb=" OE2 GLU C 231 " model vdw 2.298 2.520 ... (remaining 76272 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = 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' } 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: 0.920 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: 3.790 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.220 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.080 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 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 : 0.004 0.049 9675 Z= 0.250 Angle : 0.661 9.759 13205 Z= 0.291 Chirality : 0.048 0.143 1490 Planarity : 0.005 0.069 1620 Dihedral : 15.177 125.633 3980 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 11.88 % Favored : 88.12 % 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: -0.87 (0.27), residues: 1045 helix: -0.07 (0.57), residues: 95 sheet: -0.49 (0.25), residues: 395 loop : -0.63 (0.29), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 97 HIS 0.001 0.000 HIS A 180 PHE 0.003 0.001 PHE B 125 TYR 0.007 0.001 TYR E 89 ARG 0.003 0.000 ARG C 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.000 Fit side-chains REVERT: A 239 ARG cc_start: 0.6314 (ptm160) cc_final: 0.4596 (ptt180) REVERT: B 140 ARG cc_start: 0.7677 (ttm-80) cc_final: 0.7417 (mtp180) REVERT: B 239 ARG cc_start: 0.6186 (ptm160) cc_final: 0.4666 (ptt180) REVERT: C 103 ASP cc_start: 0.7337 (t70) cc_final: 0.7041 (t0) REVERT: D 103 ASP cc_start: 0.7270 (t70) cc_final: 0.7054 (t0) REVERT: D 212 LEU cc_start: 0.8629 (mt) cc_final: 0.8405 (mt) REVERT: D 239 ARG cc_start: 0.5887 (ptm160) cc_final: 0.5417 (ptm-80) REVERT: E 239 ARG cc_start: 0.6219 (ptm160) cc_final: 0.4521 (ptt180) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.3335 time to fit residues: 50.3451 Evaluate side-chains 97 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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-dev-5370/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-dev-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/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-dev-5370/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-dev-5370/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-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 53.5082 > 50: distance: 36 - 41: 15.612 distance: 41 - 42: 4.882 distance: 42 - 43: 16.144 distance: 42 - 45: 17.450 distance: 43 - 44: 12.562 distance: 43 - 52: 9.829 distance: 45 - 46: 22.752 distance: 46 - 47: 7.357 distance: 47 - 48: 6.801 distance: 48 - 49: 4.173 distance: 49 - 50: 7.419 distance: 49 - 51: 4.495 distance: 52 - 53: 10.127 distance: 52 - 58: 19.572 distance: 53 - 54: 6.376 distance: 53 - 56: 16.211 distance: 54 - 55: 5.170 distance: 54 - 59: 7.938 distance: 56 - 57: 12.554 distance: 57 - 58: 38.610 distance: 59 - 60: 6.327 distance: 60 - 61: 12.451 distance: 60 - 63: 5.871 distance: 61 - 62: 10.807 distance: 61 - 66: 10.395 distance: 63 - 64: 6.701 distance: 63 - 65: 9.774 distance: 66 - 67: 11.154 distance: 67 - 70: 10.795 distance: 68 - 69: 14.639 distance: 68 - 77: 7.849 distance: 70 - 71: 4.397 distance: 71 - 72: 4.828 distance: 78 - 79: 7.389 distance: 78 - 81: 6.982 distance: 79 - 80: 22.005 distance: 79 - 85: 19.795 distance: 81 - 82: 7.286 distance: 82 - 83: 11.780 distance: 82 - 84: 5.607 distance: 85 - 86: 9.580 distance: 86 - 87: 11.859 distance: 86 - 89: 19.563 distance: 87 - 88: 25.664 distance: 87 - 99: 29.194 distance: 89 - 90: 14.542 distance: 90 - 91: 11.946 distance: 90 - 92: 6.500 distance: 91 - 93: 4.223 distance: 92 - 94: 11.439 distance: 93 - 94: 4.619 distance: 95 - 97: 3.413 distance: 96 - 98: 6.004 distance: 97 - 98: 4.642 distance: 99 - 100: 13.623 distance: 100 - 101: 7.742 distance: 100 - 103: 14.236 distance: 101 - 102: 16.139 distance: 101 - 110: 25.090 distance: 103 - 104: 5.752 distance: 104 - 105: 9.250 distance: 105 - 106: 7.500 distance: 106 - 107: 5.333 distance: 107 - 109: 3.335 distance: 110 - 111: 21.067 distance: 111 - 112: 5.947 distance: 111 - 114: 14.902 distance: 112 - 113: 11.102 distance: 112 - 119: 8.772 distance: 115 - 116: 5.296 distance: 116 - 117: 3.352 distance: 117 - 118: 5.429 distance: 119 - 120: 5.172 distance: 119 - 125: 5.860 distance: 120 - 121: 3.297 distance: 120 - 123: 4.266 distance: 121 - 122: 5.008 distance: 123 - 124: 8.850 distance: 124 - 125: 3.463 distance: 126 - 127: 4.729 distance: 127 - 128: 4.576 distance: 127 - 130: 4.957 distance: 128 - 129: 4.753 distance: 128 - 133: 8.396 distance: 130 - 131: 4.252 distance: 130 - 132: 10.219