Starting phenix.real_space_refine on Sun Aug 24 17:59:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iaw_4440/08_2025/6iaw_4440.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iaw_4440/08_2025/6iaw_4440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6iaw_4440/08_2025/6iaw_4440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iaw_4440/08_2025/6iaw_4440.map" model { file = "/net/cci-nas-00/data/ceres_data/6iaw_4440/08_2025/6iaw_4440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iaw_4440/08_2025/6iaw_4440.cif" } resolution = 3.8 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= -0.000 sd= 0.660 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 73 5.16 5 C 13949 2.51 5 N 3640 2.21 5 O 4267 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21929 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3190 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 9, 'TRANS': 383} Chain: "B" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "C" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "J" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "I" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "E" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 433 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "H" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "M" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2738 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 8, 'TRANS': 329} Chain: "N" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "O" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3135 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain: "Q" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "S" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 437 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "L" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Chain: "X" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "Y" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 79 Classifications: {'peptide': 16} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 15} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 54 Classifications: {'peptide': 12} Incomplete info: {'backbone_only': 6, 'truncation_to_alanine': 6} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 275 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 55} Link IDs: {'TRANS': 54} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 55 Planarities with less than four sites: {'UNK:plan-1': 55} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 5.33, per 1000 atoms: 0.24 Number of scatterers: 21929 At special positions: 0 Unit cell: (189.214, 159.45, 120.119, 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 73 16.00 O 4267 8.00 N 3640 7.00 C 13949 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 - 3.00 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: 1.46 Conformation dependent library (CDL) restraints added in 617.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5322 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 33 sheets defined 26.8% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 8 through 16 Processing helix chain 'A' and resid 17 through 21 removed outlier: 6.310A pdb=" N ALA A 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 27 removed outlier: 4.053A pdb=" N HIS A 27 " --> pdb=" O GLN A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.582A pdb=" N LEU A 107 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N MET A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.556A pdb=" N ASN A 141 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.791A pdb=" N ALA A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 182 Processing helix chain 'A' and resid 195 through 205 removed outlier: 4.544A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.883A pdb=" N ARG A 220 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 258 removed outlier: 5.608A pdb=" N ILE A 255 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ALA A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.635A pdb=" N ILE A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 27 removed outlier: 4.153A pdb=" N HIS B 27 " --> pdb=" O GLN B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 104 through 110 removed outlier: 4.046A pdb=" N MET B 108 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 109 " --> pdb=" O GLU B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 removed outlier: 3.771A pdb=" N PHE B 142 " --> pdb=" O ARG B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 182 removed outlier: 3.580A pdb=" N TYR B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE B 163 " --> pdb=" O LYS B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 209 removed outlier: 3.690A pdb=" N SER B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 206 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 226 removed outlier: 4.269A pdb=" N ALA B 225 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 226 " --> pdb=" O GLY B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 222 through 226' Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.505A pdb=" N LYS B 247 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.585A pdb=" N ALA B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 16 Processing helix chain 'C' and resid 22 through 27 removed outlier: 4.138A pdb=" N HIS C 27 " --> pdb=" O GLN C 23 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 104 through 108 removed outlier: 4.017A pdb=" N LEU C 107 " --> pdb=" O ASN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 145 through 180 removed outlier: 5.076A pdb=" N ILE C 163 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN C 164 " --> pdb=" O ILE C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 Processing helix chain 'C' and resid 217 through 221 Processing helix chain 'C' and resid 243 through 257 removed outlier: 5.655A pdb=" N ILE C 255 " --> pdb=" O LEU C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 268 removed outlier: 4.181A pdb=" N ASP C 268 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 290 through 299 Processing helix chain 'E' and resid 13 through 17 Processing helix chain 'H' and resid 38 through 53 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 104 through 110 removed outlier: 3.501A pdb=" N LEU M 107 " --> pdb=" O ASN M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 141 removed outlier: 3.890A pdb=" N ASN M 141 " --> pdb=" O ASP M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 182 removed outlier: 3.649A pdb=" N TYR M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE M 163 " --> pdb=" O LYS M 159 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN M 164 " --> pdb=" O ILE M 160 " (cutoff:3.500A) Processing helix chain 'M' and resid 193 through 205 removed outlier: 3.513A pdb=" N ILE M 205 " --> pdb=" O VAL M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 221 Processing helix chain 'M' and resid 244 through 258 removed outlier: 5.831A pdb=" N ILE M 255 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA M 256 " --> pdb=" O ASP M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 268 removed outlier: 4.138A pdb=" N ASP M 268 " --> pdb=" O ASP M 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 265 through 268' Processing helix chain 'M' and resid 290 through 299 removed outlier: 3.620A pdb=" N ALA M 299 " --> pdb=" O ASP M 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 76 Processing helix chain 'N' and resid 104 through 110 removed outlier: 3.630A pdb=" N LEU N 107 " --> pdb=" O ASN N 104 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS N 110 " --> pdb=" O LEU N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 137 through 142 removed outlier: 3.798A pdb=" N PHE N 142 " --> pdb=" O ARG N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 182 removed outlier: 3.969A pdb=" N TYR N 156 " --> pdb=" O ALA N 152 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE N 163 " --> pdb=" O LYS N 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 209 removed outlier: 3.700A pdb=" N SER N 199 " --> pdb=" O GLU N 195 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU N 206 " --> pdb=" O PHE N 202 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLN N 209 " --> pdb=" O ILE N 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 217 through 221 Processing helix chain 'N' and resid 243 through 253 Processing helix chain 'N' and resid 266 through 268 No H-bonds generated for 'chain 'N' and resid 266 through 268' Processing helix chain 'N' and resid 290 through 299 removed outlier: 3.560A pdb=" N ALA N 299 " --> pdb=" O ASP N 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 16 through 20 removed outlier: 3.870A pdb=" N LYS O 19 " --> pdb=" O LYS O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 27 removed outlier: 3.603A pdb=" N ASN O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS O 27 " --> pdb=" O GLN O 23 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 22 through 27' Processing helix chain 'O' and resid 72 through 76 Processing helix chain 'O' and resid 106 through 110 Processing helix chain 'O' and resid 137 through 141 Processing helix chain 'O' and resid 145 through 180 removed outlier: 3.633A pdb=" N THR O 149 " --> pdb=" O LEU O 145 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ILE O 163 " --> pdb=" O LYS O 159 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN O 164 " --> pdb=" O ILE O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 198 through 205 Processing helix chain 'O' and resid 217 through 221 Processing helix chain 'O' and resid 244 through 253 Processing helix chain 'O' and resid 266 through 268 No H-bonds generated for 'chain 'O' and resid 266 through 268' Processing helix chain 'O' and resid 290 through 300 removed outlier: 3.704A pdb=" N TYR O 300 " --> pdb=" O PHE O 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 38 through 53 Processing helix chain 'X' and resid 121 through 129 removed outlier: 3.584A pdb=" N UNK X 125 " --> pdb=" O UNK X 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 38 through 53 Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 120 removed outlier: 3.664A pdb=" N GLU A 88 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N TYR A 85 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N THR C 61 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU A 87 " --> pdb=" O THR C 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 355 Processing sheet with id=AA4, first strand: chain 'A' and resid 350 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 190 removed outlier: 5.865A pdb=" N ARG A 189 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 271 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 240 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N PHE A 273 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 242 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 279 through 282 removed outlier: 4.807A pdb=" N VAL A 279 " --> pdb=" O ILE A 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 58 through 61 removed outlier: 7.557A pdb=" N GLU O 87 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N THR B 61 " --> pdb=" O GLU O 87 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.056A pdb=" N LYS B 77 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.545A pdb=" N THR B 394 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ILE B 271 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE B 240 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 280 through 282 Processing sheet with id=AB3, first strand: chain 'B' and resid 286 through 287 removed outlier: 3.841A pdb=" N PHE B 286 " --> pdb=" O ILE B 311 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 86 through 88 Processing sheet with id=AB5, first strand: chain 'C' and resid 97 through 98 Processing sheet with id=AB6, first strand: chain 'C' and resid 189 through 190 removed outlier: 3.612A pdb=" N ILE C 271 " --> pdb=" O ILE C 240 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 280 through 282 Processing sheet with id=AB8, first strand: chain 'C' and resid 286 through 287 Processing sheet with id=AB9, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AC1, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AC2, first strand: chain 'M' and resid 77 through 78 removed outlier: 3.587A pdb=" N LYS M 128 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 87 through 91 Processing sheet with id=AC4, first strand: chain 'M' and resid 188 through 190 removed outlier: 5.287A pdb=" N ARG M 189 " --> pdb=" O THR M 394 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N TYR M 341 " --> pdb=" O THR M 243 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR M 243 " --> pdb=" O TYR M 341 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 279 through 282 removed outlier: 4.665A pdb=" N VAL M 279 " --> pdb=" O ILE M 334 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 86 through 91 removed outlier: 3.587A pdb=" N GLU N 88 " --> pdb=" O LYS N 119 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 188 through 190 removed outlier: 3.615A pdb=" N THR N 394 " --> pdb=" O ARG N 189 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 240 through 241 removed outlier: 6.687A pdb=" N ILE N 240 " --> pdb=" O ILE N 271 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'N' and resid 280 through 282 Processing sheet with id=AD1, first strand: chain 'N' and resid 286 through 287 removed outlier: 3.642A pdb=" N PHE N 286 " --> pdb=" O ILE N 311 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 77 through 78 removed outlier: 5.951A pdb=" N LYS O 77 " --> pdb=" O ARG O 354 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE O 131 " --> pdb=" O HIS O 374 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 189 through 190 removed outlier: 3.563A pdb=" N THR O 394 " --> pdb=" O ARG O 189 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ILE O 271 " --> pdb=" O ILE O 238 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE O 240 " --> pdb=" O ILE O 271 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N PHE O 273 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR O 242 " --> pdb=" O PHE O 273 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 280 through 282 Processing sheet with id=AD5, first strand: chain 'L' and resid 21 through 23 Processing sheet with id=AD6, first strand: chain 'K' and resid 21 through 23 641 hydrogen bonds defined for protein. 1665 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: 3.22 Time building geometry restraints manager: 1.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6956 1.34 - 1.46: 4786 1.46 - 1.58: 10446 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 22334 Sorted by residual: bond pdb=" CG GLU M 168 " pdb=" CD GLU M 168 " ideal model delta sigma weight residual 1.516 1.464 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CA ASN A 348 " pdb=" CB ASN A 348 " ideal model delta sigma weight residual 1.532 1.565 -0.032 1.56e-02 4.11e+03 4.24e+00 bond pdb=" CA SER S 14 " pdb=" C SER S 14 " ideal model delta sigma weight residual 1.521 1.548 -0.027 1.38e-02 5.25e+03 3.94e+00 bond pdb=" CA ILE S 45 " pdb=" CB ILE S 45 " ideal model delta sigma weight residual 1.540 1.567 -0.027 1.36e-02 5.41e+03 3.84e+00 bond pdb=" CG1 ILE M 91 " pdb=" CD1 ILE M 91 " ideal model delta sigma weight residual 1.513 1.437 0.076 3.90e-02 6.57e+02 3.82e+00 ... (remaining 22329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.71: 29545 3.71 - 7.43: 536 7.43 - 11.14: 70 11.14 - 14.85: 8 14.85 - 18.57: 4 Bond angle restraints: 30163 Sorted by residual: angle pdb=" N SER E 40 " pdb=" CA SER E 40 " pdb=" C SER E 40 " ideal model delta sigma weight residual 107.23 120.29 -13.06 1.67e+00 3.59e-01 6.11e+01 angle pdb=" N GLU C 326 " pdb=" CA GLU C 326 " pdb=" C GLU C 326 " ideal model delta sigma weight residual 111.71 117.97 -6.26 1.15e+00 7.56e-01 2.96e+01 angle pdb=" CG1 ILE I 45 " pdb=" CB ILE I 45 " pdb=" CG2 ILE I 45 " ideal model delta sigma weight residual 110.70 94.48 16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C GLN S 44 " pdb=" N ILE S 45 " pdb=" CA ILE S 45 " ideal model delta sigma weight residual 121.97 131.68 -9.71 1.80e+00 3.09e-01 2.91e+01 angle pdb=" CA LEU B 183 " pdb=" CB LEU B 183 " pdb=" CG LEU B 183 " ideal model delta sigma weight residual 116.30 134.87 -18.57 3.50e+00 8.16e-02 2.81e+01 ... (remaining 30158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.76: 11955 14.76 - 29.53: 1079 29.53 - 44.29: 349 44.29 - 59.05: 34 59.05 - 73.82: 11 Dihedral angle restraints: 13428 sinusoidal: 5201 harmonic: 8227 Sorted by residual: dihedral pdb=" CA GLN I 44 " pdb=" C GLN I 44 " pdb=" N ILE I 45 " pdb=" CA ILE I 45 " ideal model delta harmonic sigma weight residual 180.00 121.63 58.37 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA GLN S 44 " pdb=" C GLN S 44 " pdb=" N ILE S 45 " pdb=" CA ILE S 45 " ideal model delta harmonic sigma weight residual 180.00 133.29 46.71 0 5.00e+00 4.00e-02 8.73e+01 dihedral pdb=" CA LEU C 206 " pdb=" C LEU C 206 " pdb=" N ASN C 207 " pdb=" CA ASN C 207 " ideal model delta harmonic sigma weight residual 180.00 141.62 38.38 0 5.00e+00 4.00e-02 5.89e+01 ... (remaining 13425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2526 0.073 - 0.145: 715 0.145 - 0.218: 102 0.218 - 0.290: 23 0.290 - 0.363: 4 Chirality restraints: 3370 Sorted by residual: chirality pdb=" CB ILE E 45 " pdb=" CA ILE E 45 " pdb=" CG1 ILE E 45 " pdb=" CG2 ILE E 45 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB ILE D 32 " pdb=" CA ILE D 32 " pdb=" CG1 ILE D 32 " pdb=" CG2 ILE D 32 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" CB ILE I 45 " pdb=" CA ILE I 45 " pdb=" CG1 ILE I 45 " pdb=" CG2 ILE I 45 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 3367 not shown) Planarity restraints: 3876 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN S 44 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C GLN S 44 " -0.074 2.00e-02 2.50e+03 pdb=" O GLN S 44 " 0.028 2.00e-02 2.50e+03 pdb=" N ILE S 45 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN I 44 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C GLN I 44 " 0.068 2.00e-02 2.50e+03 pdb=" O GLN I 44 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE I 45 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU M 168 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" CD GLU M 168 " -0.054 2.00e-02 2.50e+03 pdb=" OE1 GLU M 168 " 0.019 2.00e-02 2.50e+03 pdb=" OE2 GLU M 168 " 0.019 2.00e-02 2.50e+03 ... (remaining 3873 not shown) Histogram of nonbonded interaction distances: 1.44 - 2.13: 6 2.13 - 2.82: 7199 2.82 - 3.52: 30355 3.52 - 4.21: 51276 4.21 - 4.90: 84362 Nonbonded interactions: 173198 Sorted by model distance: nonbonded pdb=" OD2 ASP N 265 " pdb=" CD1 TYR Q 41 " model vdw 1.440 3.340 nonbonded pdb=" OD2 ASP M 265 " pdb=" CD1 TYR S 41 " model vdw 1.454 3.340 nonbonded pdb=" CG2 ILE B 261 " pdb=" OD1 ASP B 265 " model vdw 1.571 3.460 nonbonded pdb=" OD2 ASP B 265 " pdb=" CD1 TYR J 41 " model vdw 1.648 3.340 nonbonded pdb=" CG2 ILE A 261 " pdb=" OD1 ASP A 265 " model vdw 1.886 3.460 ... (remaining 173193 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 59 through 396) selection = (chain 'B' and resid 59 through 396) selection = (chain 'C' and resid 59 through 396) selection = chain 'M' selection = (chain 'N' and resid 59 through 396) selection = (chain 'O' and resid 59 through 396) } ncs_group { reference = chain 'E' selection = (chain 'I' and resid 1 through 54) selection = (chain 'J' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'X' and (resid 115 through 129 or (resid 130 and (name N or name CA or na \ me C or name O )))) selection = chain 'Y' } 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 group one per residue 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: 0.580 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: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.820 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.050 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.008 0.076 22334 Z= 0.374 Angle : 1.266 18.566 30163 Z= 0.667 Chirality : 0.067 0.363 3370 Planarity : 0.006 0.055 3876 Dihedral : 12.853 73.818 8106 Min Nonbonded Distance : 1.440 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.70 % Favored : 88.10 % Rotamer: Outliers : 1.42 % Allowed : 10.84 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.49 (0.13), residues: 2555 helix: -3.11 (0.16), residues: 519 sheet: -2.88 (0.20), residues: 455 loop : -3.10 (0.13), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 354 TYR 0.023 0.003 TYR N 121 PHE 0.025 0.003 PHE N 343 TRP 0.024 0.002 TRP C 74 HIS 0.019 0.003 HIS S 46 Details of bonding type rmsd covalent geometry : bond 0.00781 (22334) covalent geometry : angle 1.26605 (30163) hydrogen bonds : bond 0.16314 ( 627) hydrogen bonds : angle 7.82229 ( 1665) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5110 Ramachandran restraints generated. 2555 Oldfield, 0 Emsley, 2555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 832 time to evaluate : 0.537 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: A 84 GLN cc_start: 0.8585 (pt0) cc_final: 0.7567 (mp10) REVERT: A 110 LYS cc_start: 0.7472 (mmpt) cc_final: 0.7190 (mmmt) REVERT: A 127 LYS cc_start: 0.9568 (mptm) cc_final: 0.9206 (mmmm) REVERT: A 160 ILE cc_start: 0.9542 (pp) cc_final: 0.9315 (mp) REVERT: A 163 ILE cc_start: 0.9369 (pp) cc_final: 0.9108 (pt) REVERT: A 174 MET cc_start: 0.7074 (mmp) cc_final: 0.6647 (mmm) REVERT: A 194 LYS cc_start: 0.9142 (tmmt) cc_final: 0.8752 (tptt) REVERT: A 203 GLU cc_start: 0.9093 (mt-10) cc_final: 0.8853 (mt-10) REVERT: A 238 ILE cc_start: 0.9235 (pp) cc_final: 0.9003 (mp) REVERT: A 275 ASP cc_start: 0.8835 (t70) cc_final: 0.8526 (t0) REVERT: A 357 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9063 (mtpp) REVERT: B 94 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8867 (p) REVERT: B 99 MET cc_start: 0.8223 (ppp) cc_final: 0.7659 (tmm) REVERT: B 127 LYS cc_start: 0.9238 (mtpp) cc_final: 0.8629 (mmmm) REVERT: B 139 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8159 (mtp-110) REVERT: B 153 LEU cc_start: 0.8712 (tt) cc_final: 0.8419 (tt) REVERT: B 170 GLU cc_start: 0.9029 (pp20) cc_final: 0.8763 (pp20) REVERT: B 172 ARG cc_start: 0.8990 (ppt-90) cc_final: 0.8534 (ptt90) REVERT: B 220 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8209 (mtm-85) REVERT: B 238 ILE cc_start: 0.9516 (pp) cc_final: 0.9225 (mp) REVERT: B 320 ASP cc_start: 0.8821 (t0) cc_final: 0.8493 (t0) REVERT: C 45 MET cc_start: 0.7919 (mpm) cc_final: 0.7572 (mpp) REVERT: C 94 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8377 (p) REVERT: C 99 MET cc_start: 0.8372 (pmm) cc_final: 0.8164 (pmm) REVERT: C 123 ASN cc_start: 0.9251 (p0) cc_final: 0.8957 (p0) REVERT: C 170 GLU cc_start: 0.8600 (pp20) cc_final: 0.8230 (pp20) REVERT: C 172 ARG cc_start: 0.9310 (ttp80) cc_final: 0.8545 (ptt90) REVERT: C 174 MET cc_start: 0.6788 (mmp) cc_final: 0.6270 (mmp) REVERT: C 244 ASP cc_start: 0.8646 (t70) cc_final: 0.8072 (t0) REVERT: C 320 ASP cc_start: 0.8587 (t70) cc_final: 0.8295 (t70) REVERT: C 370 ASP cc_start: 0.8891 (t0) cc_final: 0.8530 (t70) REVERT: C 371 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 391 ILE cc_start: 0.9732 (OUTLIER) cc_final: 0.9489 (mm) REVERT: J 1 MET cc_start: 0.8144 (ttp) cc_final: 0.7761 (tmm) REVERT: J 23 ARG cc_start: 0.8120 (mpp-170) cc_final: 0.7714 (mpt180) REVERT: J 29 ASN cc_start: 0.7988 (t0) cc_final: 0.7568 (t0) REVERT: J 36 LYS cc_start: 0.8989 (tmmm) cc_final: 0.8743 (pttt) REVERT: J 39 ASP cc_start: 0.9038 (p0) cc_final: 0.8728 (p0) REVERT: I 5 ASN cc_start: 0.8800 (t0) cc_final: 0.8498 (t0) REVERT: I 7 MET cc_start: 0.7053 (mmm) cc_final: 0.6712 (mmm) REVERT: E 17 ASP cc_start: 0.8973 (m-30) cc_final: 0.8683 (m-30) REVERT: E 29 ASN cc_start: 0.8829 (m110) cc_final: 0.8575 (m-40) REVERT: M 63 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8899 (tm) REVERT: M 109 LEU cc_start: 0.9428 (mt) cc_final: 0.9141 (tt) REVERT: M 129 GLN cc_start: 0.8330 (tp40) cc_final: 0.7593 (tp-100) REVERT: M 159 LYS cc_start: 0.9527 (ttmp) cc_final: 0.9102 (tppt) REVERT: M 234 LYS cc_start: 0.9040 (mmmt) cc_final: 0.8487 (mmmt) REVERT: M 236 LYS cc_start: 0.9130 (mtmp) cc_final: 0.8909 (mtmm) REVERT: M 268 ASP cc_start: 0.8399 (t0) cc_final: 0.8132 (t70) REVERT: M 289 GLN cc_start: 0.8831 (mp10) cc_final: 0.8455 (mp-120) REVERT: M 291 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9015 (tp-100) REVERT: M 295 ASP cc_start: 0.9303 (p0) cc_final: 0.9005 (p0) REVERT: M 353 LYS cc_start: 0.9209 (mtpp) cc_final: 0.8821 (mtpp) REVERT: M 356 THR cc_start: 0.9267 (p) cc_final: 0.8917 (t) REVERT: M 357 LYS cc_start: 0.8898 (mptt) cc_final: 0.8666 (mmmm) REVERT: M 364 PHE cc_start: 0.9515 (t80) cc_final: 0.9224 (t80) REVERT: M 387 PHE cc_start: 0.9198 (m-80) cc_final: 0.8971 (m-80) REVERT: N 28 ASP cc_start: 0.8774 (p0) cc_final: 0.8563 (p0) REVERT: N 31 LYS cc_start: 0.9002 (tptt) cc_final: 0.8780 (mmtm) REVERT: N 45 MET cc_start: 0.8384 (pmm) cc_final: 0.8001 (mpp) REVERT: N 51 ASN cc_start: 0.9313 (m110) cc_final: 0.8938 (t0) REVERT: N 92 MET cc_start: 0.9290 (mmm) cc_final: 0.8916 (mmm) REVERT: N 94 THR cc_start: 0.9145 (p) cc_final: 0.8386 (p) REVERT: N 97 ILE cc_start: 0.9647 (tt) cc_final: 0.9276 (tp) REVERT: N 126 VAL cc_start: 0.9651 (p) cc_final: 0.9274 (p) REVERT: N 128 LYS cc_start: 0.9498 (mmmt) cc_final: 0.9294 (mmmt) REVERT: N 139 ARG cc_start: 0.8475 (mmt90) cc_final: 0.8078 (mtp-110) REVERT: N 147 ASP cc_start: 0.8920 (p0) cc_final: 0.8437 (p0) REVERT: N 156 TYR cc_start: 0.9244 (t80) cc_final: 0.8713 (t80) REVERT: N 159 LYS cc_start: 0.9215 (ptpt) cc_final: 0.8855 (ttpt) REVERT: N 172 ARG cc_start: 0.9159 (ppt-90) cc_final: 0.8953 (ptt-90) REVERT: N 217 GLU cc_start: 0.7691 (tp30) cc_final: 0.7463 (tp30) REVERT: N 228 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8552 (tm-30) REVERT: N 234 LYS cc_start: 0.9191 (mtpp) cc_final: 0.8787 (mmmt) REVERT: N 237 ASP cc_start: 0.8643 (p0) cc_final: 0.7746 (p0) REVERT: N 281 LYS cc_start: 0.9239 (tptp) cc_final: 0.8760 (tptp) REVERT: N 291 GLN cc_start: 0.9176 (tp40) cc_final: 0.8325 (tm-30) REVERT: N 295 ASP cc_start: 0.9435 (p0) cc_final: 0.8679 (p0) REVERT: N 302 ASP cc_start: 0.8739 (t0) cc_final: 0.8370 (t70) REVERT: N 304 GLN cc_start: 0.8394 (pp30) cc_final: 0.8084 (pp30) REVERT: N 309 ASP cc_start: 0.7553 (m-30) cc_final: 0.7276 (m-30) REVERT: N 346 ASP cc_start: 0.8882 (p0) cc_final: 0.8506 (p0) REVERT: N 387 PHE cc_start: 0.8971 (m-10) cc_final: 0.8547 (m-10) REVERT: O 39 TRP cc_start: 0.9345 (t-100) cc_final: 0.9130 (t-100) REVERT: O 79 GLN cc_start: 0.8556 (mm110) cc_final: 0.8222 (mm110) REVERT: O 97 ILE cc_start: 0.9375 (pp) cc_final: 0.8849 (pp) REVERT: O 108 MET cc_start: 0.8542 (ptm) cc_final: 0.8043 (mtt) REVERT: O 167 GLU cc_start: 0.8475 (tp30) cc_final: 0.7966 (tp30) REVERT: O 203 GLU cc_start: 0.8792 (pp20) cc_final: 0.8471 (pp20) REVERT: O 236 LYS cc_start: 0.9145 (pttp) cc_final: 0.8917 (ptpt) REVERT: O 238 ILE cc_start: 0.9114 (pp) cc_final: 0.8898 (mp) REVERT: O 261 ILE cc_start: 0.5920 (OUTLIER) cc_final: 0.4734 (pp) REVERT: Q 20 LEU cc_start: 0.9085 (tt) cc_final: 0.8537 (tt) REVERT: Q 21 ASN cc_start: 0.8282 (t0) cc_final: 0.8026 (t0) REVERT: Q 23 ARG cc_start: 0.8263 (pmm150) cc_final: 0.8002 (pmt170) REVERT: Q 33 ASP cc_start: 0.8282 (t70) cc_final: 0.7945 (t70) REVERT: S 10 MET cc_start: 0.8315 (mpt) cc_final: 0.7812 (mmm) REVERT: S 14 SER cc_start: 0.6663 (m) cc_final: 0.5382 (m) REVERT: S 39 ASP cc_start: 0.8295 (p0) cc_final: 0.8050 (p0) REVERT: S 49 SER cc_start: 0.8937 (t) cc_final: 0.8655 (p) outliers start: 33 outliers final: 2 residues processed: 849 average time/residue: 0.1648 time to fit residues: 205.3689 Evaluate side-chains 594 residues out of total 2324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 587 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain M residue 63 LEU Chi-restraints excluded: chain O residue 261 ILE Chi-restraints excluded: chain S residue 34 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.5263 > 50: distance: 17 - 22: 7.708 distance: 22 - 23: 17.980 distance: 23 - 24: 10.539 distance: 23 - 26: 10.558 distance: 24 - 25: 9.400 distance: 24 - 30: 26.991 distance: 26 - 27: 22.991 distance: 27 - 29: 22.648 distance: 30 - 31: 7.430 distance: 31 - 32: 21.807 distance: 31 - 34: 5.181 distance: 32 - 33: 22.202 distance: 32 - 39: 22.633 distance: 34 - 35: 17.315 distance: 35 - 36: 19.650 distance: 36 - 37: 9.344 distance: 37 - 38: 19.441 distance: 39 - 40: 9.090 distance: 39 - 45: 24.838 distance: 40 - 41: 13.820 distance: 40 - 43: 24.608 distance: 41 - 42: 36.465 distance: 41 - 46: 18.213 distance: 43 - 44: 17.249 distance: 44 - 45: 3.001 distance: 46 - 47: 14.993 distance: 46 - 52: 17.487 distance: 47 - 48: 22.349 distance: 47 - 50: 23.683 distance: 48 - 49: 30.265 distance: 48 - 53: 27.547 distance: 50 - 51: 25.298 distance: 51 - 52: 32.316 distance: 53 - 54: 35.285 distance: 54 - 55: 28.834 distance: 54 - 57: 14.339 distance: 55 - 56: 10.854 distance: 55 - 64: 13.362 distance: 57 - 58: 13.507 distance: 58 - 59: 4.679 distance: 64 - 65: 13.018 distance: 65 - 66: 3.575 distance: 65 - 68: 33.253 distance: 66 - 67: 4.056 distance: 66 - 74: 16.110 distance: 68 - 69: 15.307 distance: 69 - 70: 10.838 distance: 69 - 71: 27.919 distance: 70 - 72: 19.081 distance: 74 - 75: 12.535 distance: 75 - 76: 27.806 distance: 75 - 78: 20.773 distance: 76 - 77: 21.469 distance: 79 - 81: 3.974 distance: 82 - 83: 21.305 distance: 82 - 88: 43.554 distance: 83 - 84: 4.564 distance: 83 - 86: 10.630 distance: 84 - 85: 16.708 distance: 84 - 89: 5.128 distance: 86 - 87: 48.757 distance: 89 - 90: 5.264 distance: 90 - 91: 22.006 distance: 91 - 92: 9.876 distance: 91 - 98: 23.376 distance: 94 - 95: 24.042 distance: 95 - 96: 56.568 distance: 95 - 97: 26.035 distance: 98 - 99: 14.322 distance: 99 - 100: 17.897 distance: 99 - 102: 9.411 distance: 100 - 101: 16.400 distance: 100 - 109: 19.910 distance: 102 - 103: 9.258 distance: 103 - 104: 29.076 distance: 103 - 105: 15.659 distance: 105 - 107: 12.197 distance: 106 - 108: 6.562 distance: 107 - 108: 27.049