Starting phenix.real_space_refine on Tue May 5 04:35:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ub1_63999/05_2026/9ub1_63999.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ub1_63999/05_2026/9ub1_63999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ub1_63999/05_2026/9ub1_63999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ub1_63999/05_2026/9ub1_63999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ub1_63999/05_2026/9ub1_63999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ub1_63999/05_2026/9ub1_63999.map" } resolution = 2.35 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 132 5.16 5 C 16184 2.51 5 N 4412 2.21 5 O 5280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26012 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3008 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 372} Chain: "E" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1727 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 12, 'TRANS': 215} Chain: "F" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1631 Classifications: {'peptide': 212} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200} Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' CA': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Restraints were copied for chains: B, C, D, G, I, K, H, J, L, N, O, P Time building chain proxies: 4.44, per 1000 atoms: 0.17 Number of scatterers: 26012 At special positions: 0 Unit cell: (189.75, 189.75, 112.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 132 16.00 O 5280 8.00 N 4412 7.00 C 16184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 437 " distance=2.03 Simple disulfide: pdb=" SG CYS A 144 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 250 " distance=2.03 Simple disulfide: pdb=" SG CYS A 252 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 298 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 309 " distance=2.03 Simple disulfide: pdb=" SG CYS A 338 " - pdb=" SG CYS A 357 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" CA CYS B 195 " - pdb=" SG CYS B 195 " distance=2.82 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 437 " distance=2.03 Simple disulfide: pdb=" SG CYS C 112 " - pdb=" SG CYS C 437 " distance=2.03 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 437 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 213 " distance=2.03 Simple disulfide: pdb=" SG CYS C 195 " - pdb=" SG CYS C 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 195 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS B 203 " - pdb=" SG CYS B 250 " distance=2.03 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 250 " distance=2.03 Simple disulfide: pdb=" SG CYS D 203 " - pdb=" SG CYS D 250 " distance=2.03 Simple disulfide: pdb=" SG CYS B 252 " - pdb=" SG CYS B 257 " distance=2.03 Simple disulfide: pdb=" SG CYS C 252 " - pdb=" SG CYS C 257 " distance=2.03 Simple disulfide: pdb=" SG CYS D 252 " - pdb=" SG CYS D 257 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 311 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS D 298 " - pdb=" SG CYS D 311 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 309 " distance=2.03 Simple disulfide: pdb=" SG CYS C 300 " - pdb=" SG CYS C 309 " distance=2.03 Simple disulfide: pdb=" SG CYS D 300 " - pdb=" SG CYS D 309 " distance=2.03 Simple disulfide: pdb=" SG CYS B 338 " - pdb=" SG CYS B 357 " distance=2.03 Simple disulfide: pdb=" SG CYS C 338 " - pdb=" SG CYS C 357 " distance=2.03 Simple disulfide: pdb=" SG CYS D 338 " - pdb=" SG CYS D 357 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 467 " distance=2.03 Simple disulfide: pdb=" SG CYS C 441 " - pdb=" SG CYS C 467 " distance=2.03 Simple disulfide: pdb=" SG CYS D 441 " - pdb=" SG CYS D 467 " 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 Links applied ALPHA1-2 " MAN M 4 " - " MAN M 5 " " MAN N 4 " - " MAN N 5 " " MAN O 4 " - " MAN O 5 " " MAN P 4 " - " MAN P 5 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " MAN M 6 " - " MAN M 7 " " BMA N 3 " - " MAN N 4 " " MAN N 6 " - " MAN N 7 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " ALPHA1-6 " BMA M 3 " - " MAN M 6 " " MAN M 6 " - " MAN M 8 " " BMA N 3 " - " MAN N 6 " " MAN N 6 " - " MAN N 8 " " BMA O 3 " - " MAN O 6 " " MAN O 6 " - " MAN O 8 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " NAG-ASN " NAG A 501 " - " ASN A 166 " " NAG A 502 " - " ASN A 254 " " NAG A 503 " - " ASN A 349 " " NAG B 501 " - " ASN B 166 " " NAG B 502 " - " ASN B 254 " " NAG B 503 " - " ASN B 349 " " NAG C 501 " - " ASN C 166 " " NAG C 502 " - " ASN C 254 " " NAG C 503 " - " ASN C 349 " " NAG D 501 " - " ASN D 166 " " NAG D 502 " - " ASN D 254 " " NAG D 503 " - " ASN D 349 " " NAG M 1 " - " ASN A 220 " " NAG N 1 " - " ASN B 220 " " NAG O 1 " - " ASN C 220 " " NAG P 1 " - " ASN D 220 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 962.7 milliseconds 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6048 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 68 sheets defined 5.0% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.547A pdb=" N LEU A 128 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.547A pdb=" N SER A 165 " --> pdb=" O ASN A 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN A 166 " --> pdb=" O VAL A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 162 through 166' Processing helix chain 'B' and resid 124 through 129 removed outlier: 3.546A pdb=" N LEU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 removed outlier: 3.546A pdb=" N SER B 165 " --> pdb=" O ASN B 162 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN B 166 " --> pdb=" O VAL B 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 162 through 166' Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.546A pdb=" N LEU C 128 " --> pdb=" O ASN C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 166 removed outlier: 3.548A pdb=" N SER C 165 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASN C 166 " --> pdb=" O VAL C 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 162 through 166' Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.546A pdb=" N LEU D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 166 removed outlier: 3.547A pdb=" N SER D 165 " --> pdb=" O ASN D 162 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASN D 166 " --> pdb=" O VAL D 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 162 through 166' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR E 91 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 205 Processing helix chain 'E' and resid 214 through 217 Processing helix chain 'F' and resid 121 through 128 removed outlier: 3.507A pdb=" N LEU F 125 " --> pdb=" O SER F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 188 removed outlier: 4.076A pdb=" N GLU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR G 91 " --> pdb=" O VAL G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 199 through 205 Processing helix chain 'G' and resid 214 through 217 Processing helix chain 'H' and resid 121 through 128 removed outlier: 3.507A pdb=" N LEU H 125 " --> pdb=" O SER H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 188 removed outlier: 4.076A pdb=" N GLU H 187 " --> pdb=" O LYS H 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.607A pdb=" N THR I 91 " --> pdb=" O VAL I 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 205 Processing helix chain 'I' and resid 214 through 217 Processing helix chain 'J' and resid 121 through 128 removed outlier: 3.508A pdb=" N LEU J 125 " --> pdb=" O SER J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 188 removed outlier: 4.076A pdb=" N GLU J 187 " --> pdb=" O LYS J 183 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR K 91 " --> pdb=" O VAL K 88 " (cutoff:3.500A) Processing helix chain 'K' and resid 199 through 205 Processing helix chain 'K' and resid 214 through 217 Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.507A pdb=" N LEU L 125 " --> pdb=" O SER L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 4.077A pdb=" N GLU L 187 " --> pdb=" O LYS L 183 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 116 through 122 removed outlier: 4.065A pdb=" N GLY A 116 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL A 465 " --> pdb=" O PHE A 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS A 122 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE A 463 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG A 440 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 135 through 144 removed outlier: 4.877A pdb=" N TRP A 135 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR A 158 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR A 137 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS A 156 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU A 139 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU A 154 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 177 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 178 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS A 192 " --> pdb=" O MET A 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR A 227 " --> pdb=" O LEU A 231 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU A 231 " --> pdb=" O TYR A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 243 through 244 removed outlier: 4.011A pdb=" N VAL A 251 " --> pdb=" O THR A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU A 278 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 303 removed outlier: 5.671A pdb=" N GLU A 297 " --> pdb=" O ARG A 312 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG A 312 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 376 removed outlier: 5.841A pdb=" N LEU A 392 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N ARG A 420 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR A 396 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL A 416 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS A 398 " --> pdb=" O ARG A 414 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG A 414 " --> pdb=" O LYS A 398 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 116 through 122 removed outlier: 4.065A pdb=" N GLY B 116 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B 465 " --> pdb=" O PHE B 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS B 122 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE B 463 " --> pdb=" O LYS B 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG B 440 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 135 through 144 removed outlier: 4.877A pdb=" N TRP B 135 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N THR B 158 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR B 137 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS B 156 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU B 139 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 154 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR B 177 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 178 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS B 192 " --> pdb=" O MET B 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR B 227 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LEU B 231 " --> pdb=" O TYR B 227 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 243 through 244 removed outlier: 4.009A pdb=" N VAL B 251 " --> pdb=" O THR B 258 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU B 278 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 296 through 303 removed outlier: 5.670A pdb=" N GLU B 297 " --> pdb=" O ARG B 312 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG B 312 " --> pdb=" O GLU B 297 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 373 through 376 removed outlier: 5.842A pdb=" N LEU B 392 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N ARG B 420 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B 396 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL B 416 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS B 398 " --> pdb=" O ARG B 414 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG B 414 " --> pdb=" O LYS B 398 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 116 through 122 removed outlier: 4.064A pdb=" N GLY C 116 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C 465 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N LYS C 122 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE C 463 " --> pdb=" O LYS C 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 440 " --> pdb=" O GLY C 468 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 135 through 144 removed outlier: 4.877A pdb=" N TRP C 135 " --> pdb=" O THR C 158 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR C 158 " --> pdb=" O TRP C 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR C 137 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LYS C 156 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU C 139 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU C 154 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR C 177 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU C 178 " --> pdb=" O VAL C 194 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS C 192 " --> pdb=" O MET C 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR C 227 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 231 " --> pdb=" O TYR C 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 243 through 244 removed outlier: 4.011A pdb=" N VAL C 251 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU C 278 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 296 through 303 removed outlier: 5.671A pdb=" N GLU C 297 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG C 312 " --> pdb=" O GLU C 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 373 through 376 removed outlier: 5.841A pdb=" N LEU C 392 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG C 420 " --> pdb=" O LEU C 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR C 396 " --> pdb=" O VAL C 416 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL C 416 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS C 398 " --> pdb=" O ARG C 414 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG C 414 " --> pdb=" O LYS C 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 116 through 122 removed outlier: 4.065A pdb=" N GLY D 116 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL D 465 " --> pdb=" O PHE D 120 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS D 122 " --> pdb=" O ILE D 463 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE D 463 " --> pdb=" O LYS D 122 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG D 440 " --> pdb=" O GLY D 468 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 135 through 144 removed outlier: 4.876A pdb=" N TRP D 135 " --> pdb=" O THR D 158 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N THR D 158 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR D 137 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LYS D 156 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLU D 139 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D 154 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR D 177 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU D 178 " --> pdb=" O VAL D 194 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LYS D 192 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 199 through 204 removed outlier: 6.450A pdb=" N TYR D 227 " --> pdb=" O LEU D 231 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU D 231 " --> pdb=" O TYR D 227 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 243 through 244 removed outlier: 4.009A pdb=" N VAL D 251 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 243 through 244 removed outlier: 6.482A pdb=" N GLU D 278 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE D 282 " --> pdb=" O GLU D 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 296 through 303 removed outlier: 5.671A pdb=" N GLU D 297 " --> pdb=" O ARG D 312 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ARG D 312 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 373 through 376 removed outlier: 5.842A pdb=" N LEU D 392 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG D 420 " --> pdb=" O LEU D 392 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR D 396 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL D 416 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N LYS D 398 " --> pdb=" O ARG D 414 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ARG D 414 " --> pdb=" O LYS D 398 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.149A pdb=" N GLY E 10 " --> pdb=" O THR E 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AD5, first strand: chain 'E' and resid 133 through 137 Processing sheet with id=AD6, first strand: chain 'E' and resid 164 through 167 removed outlier: 4.233A pdb=" N TYR E 207 " --> pdb=" O VAL E 224 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AD8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.995A pdb=" N LEU F 33 " --> pdb=" O HIS F 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 10 through 13 removed outlier: 4.054A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR F 173 " --> pdb=" O ASN F 138 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 145 through 150 Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.149A pdb=" N GLY G 10 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 133 through 137 Processing sheet with id=AE6, first strand: chain 'G' and resid 133 through 137 Processing sheet with id=AE7, first strand: chain 'G' and resid 164 through 167 removed outlier: 4.233A pdb=" N TYR G 207 " --> pdb=" O VAL G 224 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AE9, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.995A pdb=" N LEU H 33 " --> pdb=" O HIS H 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 13 removed outlier: 4.055A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR H 173 " --> pdb=" O ASN H 138 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 145 through 150 Processing sheet with id=AF4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.148A pdb=" N GLY I 10 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 133 through 137 Processing sheet with id=AF7, first strand: chain 'I' and resid 133 through 137 Processing sheet with id=AF8, first strand: chain 'I' and resid 164 through 167 removed outlier: 4.234A pdb=" N TYR I 207 " --> pdb=" O VAL I 224 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.996A pdb=" N LEU J 33 " --> pdb=" O HIS J 49 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N HIS J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 10 through 13 removed outlier: 4.055A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR J 173 " --> pdb=" O ASN J 138 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 145 through 150 Processing sheet with id=AG5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.149A pdb=" N GLY K 10 " --> pdb=" O THR K 123 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 133 through 137 Processing sheet with id=AG8, first strand: chain 'K' and resid 133 through 137 Processing sheet with id=AG9, first strand: chain 'K' and resid 164 through 167 removed outlier: 4.233A pdb=" N TYR K 207 " --> pdb=" O VAL K 224 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.994A pdb=" N LEU L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N HIS L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 13 removed outlier: 4.054A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.952A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 145 through 150 996 hydrogen bonds defined for protein. 2664 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: 5.45 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8436 1.35 - 1.47: 6960 1.47 - 1.60: 11032 1.60 - 1.72: 0 1.72 - 1.85: 160 Bond restraints: 26588 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.31e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.26e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 ... (remaining 26583 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 35124 2.07 - 4.15: 833 4.15 - 6.22: 127 6.22 - 8.30: 24 8.30 - 10.37: 4 Bond angle restraints: 36112 Sorted by residual: angle pdb=" CB GLU L 165 " pdb=" CG GLU L 165 " pdb=" CD GLU L 165 " ideal model delta sigma weight residual 112.60 118.51 -5.91 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CB GLU F 165 " pdb=" CG GLU F 165 " pdb=" CD GLU F 165 " ideal model delta sigma weight residual 112.60 118.50 -5.90 1.70e+00 3.46e-01 1.20e+01 angle pdb=" CB GLU J 165 " pdb=" CG GLU J 165 " pdb=" CD GLU J 165 " ideal model delta sigma weight residual 112.60 118.49 -5.89 1.70e+00 3.46e-01 1.20e+01 angle pdb=" CB GLU H 165 " pdb=" CG GLU H 165 " pdb=" CD GLU H 165 " ideal model delta sigma weight residual 112.60 118.46 -5.86 1.70e+00 3.46e-01 1.19e+01 angle pdb=" C HIS A 356 " pdb=" N CYS A 357 " pdb=" CA CYS A 357 " ideal model delta sigma weight residual 122.08 126.94 -4.86 1.47e+00 4.63e-01 1.09e+01 ... (remaining 36107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.21: 15385 22.21 - 44.41: 731 44.41 - 66.62: 212 66.62 - 88.82: 55 88.82 - 111.03: 16 Dihedral angle restraints: 16399 sinusoidal: 6923 harmonic: 9476 Sorted by residual: dihedral pdb=" CB CYS B 195 " pdb=" CA CYS B 195 " pdb=" SG CYS B 195 " pdb=" CB CYS B 195 " ideal model delta sinusoidal sigma weight residual -86.00 0.00 -86.00 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CA CYS A 357 " pdb=" C CYS A 357 " pdb=" N LEU A 358 " pdb=" CA LEU A 358 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS D 357 " pdb=" C CYS D 357 " pdb=" N LEU D 358 " pdb=" CA LEU D 358 " ideal model delta harmonic sigma weight residual 180.00 153.87 26.13 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 16396 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 4096 0.337 - 0.673: 20 0.673 - 1.010: 4 1.010 - 1.347: 0 1.347 - 1.683: 4 Chirality restraints: 4124 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.08e+03 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.08e+03 chirality pdb=" C1 BMA P 3 " pdb=" O4 NAG P 2 " pdb=" C2 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.08e+03 ... (remaining 4121 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 145 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.99e+00 pdb=" N PRO B 146 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 145 " -0.029 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO C 146 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 146 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 146 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 145 " 0.029 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO A 146 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 146 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 146 " 0.024 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 281 2.61 - 3.18: 20430 3.18 - 3.75: 35782 3.75 - 4.33: 53268 4.33 - 4.90: 90757 Nonbonded interactions: 200518 Sorted by model distance: nonbonded pdb=" SG CYS H 134 " pdb=" SG CYS H 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS F 134 " pdb=" SG CYS F 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS J 134 " pdb=" SG CYS J 194 " model vdw 2.036 3.760 nonbonded pdb=" SG CYS K 153 " pdb=" SG CYS K 209 " model vdw 2.038 3.760 ... (remaining 200513 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } 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: 4.310 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.150 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 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 : 0.007 0.791 26669 Z= 0.349 Angle : 1.293 74.766 36318 Z= 0.577 Chirality : 0.087 1.683 4124 Planarity : 0.004 0.043 4600 Dihedral : 15.050 111.030 10240 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.69 % Allowed : 5.69 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: -2.23 (0.13), residues: 3288 helix: -3.17 (0.37), residues: 76 sheet: -0.24 (0.13), residues: 1448 loop : -2.59 (0.12), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 211 TYR 0.016 0.002 TYR G 109 PHE 0.017 0.002 PHE C 374 TRP 0.019 0.001 TRP B 198 HIS 0.004 0.001 HIS J 189 Details of bonding type rmsd covalent geometry : bond 0.00518 (26588) covalent geometry : angle 0.79446 (36112) SS BOND : bond 0.12999 ( 37) SS BOND : angle 11.92139 ( 74) hydrogen bonds : bond 0.13317 ( 912) hydrogen bonds : angle 7.16600 ( 2664) link_ALPHA1-2 : bond 0.06505 ( 4) link_ALPHA1-2 : angle 18.41670 ( 12) link_ALPHA1-3 : bond 0.06537 ( 8) link_ALPHA1-3 : angle 15.32606 ( 24) link_ALPHA1-6 : bond 0.06565 ( 8) link_ALPHA1-6 : angle 16.33467 ( 24) link_BETA1-4 : bond 0.06473 ( 8) link_BETA1-4 : angle 21.23483 ( 24) link_NAG-ASN : bond 0.00197 ( 16) link_NAG-ASN : angle 3.12863 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6576 Ramachandran restraints generated. 3288 Oldfield, 0 Emsley, 3288 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 288 time to evaluate : 1.002 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 164 outliers final: 17 residues processed: 422 average time/residue: 0.8005 time to fit residues: 379.2194 Evaluate side-chains 191 residues out of total 2884 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain B residue 237 SER Chi-restraints excluded: chain B residue 462 SER Chi-restraints excluded: chain C residue 237 SER Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 462 SER Chi-restraints excluded: chain E residue 63 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain G residue 63 SER Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 143 SER Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 128 SER Chi-restraints excluded: chain K residue 143 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/iotbx/cli_parser.py", line 995, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/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-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1590, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1493, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1374, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1482 > 50: distance: 122 - 129: 4.602 distance: 129 - 130: 5.329 distance: 129 - 200: 6.219 distance: 130 - 131: 5.602 distance: 130 - 133: 4.279 distance: 131 - 132: 5.778 distance: 133 - 134: 4.332 distance: 134 - 135: 3.701 distance: 135 - 136: 5.458 distance: 135 - 137: 4.074 distance: 138 - 139: 3.703 distance: 140 - 150: 5.417 distance: 143 - 144: 5.247 distance: 143 - 145: 4.230 distance: 144 - 146: 5.715 distance: 145 - 147: 3.412 distance: 146 - 148: 3.743 distance: 148 - 149: 3.699 distance: 150 - 151: 5.636 distance: 151 - 154: 3.739 distance: 152 - 153: 4.217 distance: 152 - 161: 5.786 distance: 154 - 155: 5.563 distance: 155 - 157: 3.503 distance: 156 - 158: 5.592 distance: 157 - 159: 6.980 distance: 158 - 160: 11.898 distance: 159 - 160: 3.411 distance: 162 - 163: 5.840 distance: 162 - 165: 5.677 distance: 163 - 164: 3.281 distance: 163 - 170: 4.229 distance: 165 - 166: 7.735 distance: 166 - 167: 8.210 distance: 167 - 168: 9.446 distance: 168 - 169: 8.636 distance: 171 - 172: 6.783 distance: 171 - 174: 3.761 distance: 172 - 173: 3.187 distance: 172 - 178: 4.835 distance: 174 - 175: 8.228 distance: 175 - 177: 6.732 distance: 178 - 184: 4.485 distance: 179 - 182: 3.509 distance: 180 - 181: 7.304 distance: 182 - 183: 6.613 distance: 183 - 184: 6.130 distance: 185 - 186: 3.933 distance: 186 - 187: 3.782 distance: 186 - 189: 6.025 distance: 187 - 188: 8.052 distance: 187 - 197: 5.239 distance: 189 - 190: 4.748 distance: 190 - 191: 9.947 distance: 190 - 192: 5.030 distance: 191 - 193: 10.084 distance: 192 - 194: 6.166 distance: 193 - 195: 6.082 distance: 195 - 196: 6.642 distance: 198 - 199: 3.485 distance: 199 - 200: 3.537 distance: 199 - 204: 3.670 distance: 201 - 202: 5.846 distance: 201 - 203: 7.111 distance: 205 - 206: 7.735 distance: 206 - 207: 8.604 distance: 206 - 215: 17.871 distance: 208 - 209: 4.622 distance: 209 - 211: 4.800 distance: 210 - 212: 8.203 distance: 211 - 213: 9.795 distance: 212 - 214: 7.765 distance: 213 - 214: 3.709 distance: 215 - 216: 12.761 distance: 216 - 217: 40.194 distance: 217 - 218: 18.153 distance: 217 - 219: 14.487