Starting phenix.real_space_refine on Thu Feb 5 11:02:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n4e_48873/02_2026/9n4e_48873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n4e_48873/02_2026/9n4e_48873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9n4e_48873/02_2026/9n4e_48873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n4e_48873/02_2026/9n4e_48873.map" model { file = "/net/cci-nas-00/data/ceres_data/9n4e_48873/02_2026/9n4e_48873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n4e_48873/02_2026/9n4e_48873.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.019 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 84 5.16 5 C 10410 2.51 5 N 2913 2.21 5 O 3255 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16662 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 296} Conformer: "B" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 296} bond proxies already assigned to first conformer: 2473 Chain: "C" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 296} Conformer: "B" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 296} bond proxies already assigned to first conformer: 2473 Chain: "E" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 296} Conformer: "B" Number of residues, atoms: 316, 2437 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 296} bond proxies already assigned to first conformer: 2473 Chain: "K" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 121} Chain: "M" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 95} Chain: "O" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 121} Chain: "P" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 95} Chain: "Q" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 971 Classifications: {'peptide': 125} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 121} Chain: "R" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 785 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 95} Chain: "B" Number of atoms: 1343 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "D" Number of atoms: 1343 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Chain: "F" Number of atoms: 1343 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 163, 1337 Classifications: {'peptide': 163} Link IDs: {'TRANS': 162} Chain breaks: 1 bond proxies already assigned to first conformer: 1352 Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ASER A 227 " occ=0.26 ... (10 atoms not shown) pdb=" OG BSER A 227 " occ=0.74 residue: pdb=" N AGLY A 228 " occ=0.26 ... (6 atoms not shown) pdb=" O BGLY A 228 " occ=0.74 residue: pdb=" N AMET A 260 " occ=0.42 ... (14 atoms not shown) pdb=" CE BMET A 260 " occ=0.58 residue: pdb=" N ASER C 227 " occ=0.53 ... (10 atoms not shown) pdb=" OG BSER C 227 " occ=0.47 residue: pdb=" N AGLY C 228 " occ=0.53 ... (6 atoms not shown) pdb=" O BGLY C 228 " occ=0.47 residue: pdb=" N AMET C 260 " occ=0.37 ... (14 atoms not shown) pdb=" CE BMET C 260 " occ=0.63 residue: pdb=" N ASER E 227 " occ=0.48 ... (10 atoms not shown) pdb=" OG BSER E 227 " occ=0.52 residue: pdb=" N AGLY E 228 " occ=0.48 ... (6 atoms not shown) pdb=" O BGLY E 228 " occ=0.52 residue: pdb=" N AMET E 260 " occ=0.28 ... (14 atoms not shown) pdb=" CE BMET E 260 " occ=0.72 residue: pdb=" N ASER B 40 " occ=0.75 ... (10 atoms not shown) pdb=" OG BSER B 40 " occ=0.25 residue: pdb=" N ASER D 40 " occ=0.75 ... (10 atoms not shown) pdb=" OG BSER D 40 " occ=0.25 residue: pdb=" N ASER F 40 " occ=0.75 ... (10 atoms not shown) pdb=" OG BSER F 40 " occ=0.25 Time building chain proxies: 5.03, per 1000 atoms: 0.30 Number of scatterers: 16662 At special positions: 0 Unit cell: (138.069, 137.54, 147.591, 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 84 16.00 O 3255 8.00 N 2913 7.00 C 10410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS D 137 " distance=2.04 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.03 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.03 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.03 Simple disulfide: pdb=" SG CYS E 14 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 92 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.31 Conformation dependent library (CDL) restraints added in 958.3 milliseconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 50 sheets defined 21.4% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.644A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 79 " --> pdb=" O CYS A 76 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 136 through 140 removed outlier: 4.077A pdb=" N LYS A 140 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 77 removed outlier: 3.589A pdb=" N ASP C 77 " --> pdb=" O PRO C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 136 through 138 No H-bonds generated for 'chain 'C' and resid 136 through 138' Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.589A pdb=" N ASP E 77 " --> pdb=" O PRO E 74 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE E 79 " --> pdb=" O CYS E 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 196 Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.783A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'M' and resid 29 through 31 No H-bonds generated for 'chain 'M' and resid 29 through 31' Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.837A pdb=" N PHE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.789A pdb=" N TYR O 32 " --> pdb=" O PHE O 29 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 removed outlier: 3.501A pdb=" N THR O 87 " --> pdb=" O SER O 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 31 No H-bonds generated for 'chain 'P' and resid 29 through 31' Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.802A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 32 removed outlier: 3.688A pdb=" N TYR Q 32 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 83 through 87 Processing helix chain 'R' and resid 29 through 31 No H-bonds generated for 'chain 'R' and resid 29 through 31' Processing helix chain 'R' and resid 79 through 83 removed outlier: 3.839A pdb=" N PHE R 83 " --> pdb=" O PRO R 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 removed outlier: 3.528A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 127 Processing helix chain 'B' and resid 145 through 155 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'D' and resid 38 through 56 removed outlier: 3.578A pdb=" N VAL D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 127 Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 162 through 171 Processing helix chain 'F' and resid 37 through 56 removed outlier: 3.712A pdb=" N ARG F 54 " --> pdb=" O GLY F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 127 Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 162 through 171 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.403A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 58 through 60 Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.096A pdb=" N VAL A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLY A 256 " --> pdb=" O VAL A 179 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.663A pdb=" N VAL A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 removed outlier: 5.328A pdb=" N ARG A 201 " --> pdb=" O ASN A 248 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 286 through 287 removed outlier: 3.902A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 12 through 17 removed outlier: 3.574A pdb=" N GLY C 16 " --> pdb=" O GLY D 23 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N TYR D 22 " --> pdb=" O ASP D 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.601A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.718A pdb=" N LEU C 59 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.117A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VAL C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY C 256 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.117A pdb=" N ASP C 101 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 9.161A pdb=" N TRP C 234 " --> pdb=" O ASP C 101 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 removed outlier: 5.600A pdb=" N ARG C 201 " --> pdb=" O ASN C 248 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 286 through 288 removed outlier: 4.142A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 62 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 31 through 36 Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.550A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 60 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 101 removed outlier: 5.047A pdb=" N VAL E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY E 256 " --> pdb=" O VAL E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.573A pdb=" N VAL E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 169 removed outlier: 5.591A pdb=" N ARG E 201 " --> pdb=" O ASN E 248 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 286 through 287 removed outlier: 3.639A pdb=" N LYS F 62 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AD9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.862A pdb=" N TRP K 36 " --> pdb=" O MET K 48 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N TYR K 33 " --> pdb=" O GLY K 95 " (cutoff:3.500A) Sorry: Error in SS definitions, most likely atoms are absent for one of them.