Starting phenix.real_space_refine on Sun Aug 24 06:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f6z_28893/08_2025/8f6z_28893.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f6z_28893/08_2025/8f6z_28893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f6z_28893/08_2025/8f6z_28893.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f6z_28893/08_2025/8f6z_28893.map" model { file = "/net/cci-nas-00/data/ceres_data/8f6z_28893/08_2025/8f6z_28893.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f6z_28893/08_2025/8f6z_28893.cif" } resolution = 2.7 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= 0.003 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 P 5 5.49 5 S 85 5.16 5 C 11129 2.51 5 N 2640 2.21 5 O 3138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s 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: 16997 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 366} Chain breaks: 1 Chain: "B" Number of atoms: 3456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3456 Classifications: {'peptide': 425} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 397} Chain breaks: 1 Chain: "C" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3294 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 382} Chain breaks: 1 Chain: "D" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3151 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 367} Chain breaks: 1 Chain: "E" Number of atoms: 3317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3317 Classifications: {'peptide': 409} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 386} Chain breaks: 1 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'CLR': 1, 'SCK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 60 Unusual residues: {'DD9': 1, 'NAG': 1, 'POV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'CLR': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'POV:plan-1': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'CLR': 1, 'POV': 1, 'SCK': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'NAG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" C1 CLR A 502 " occ=0.80 ... (26 atoms not shown) pdb=" O1 CLR A 502 " occ=0.80 residue: pdb=" N POV B 602 " occ=0.75 ... (35 atoms not shown) pdb="C311 POV B 602 " occ=0.75 residue: pdb=" C1 CLR C 501 " occ=0.89 ... (26 atoms not shown) pdb=" O1 CLR C 501 " occ=0.89 residue: pdb=" C1 CLR D 503 " occ=0.75 ... (26 atoms not shown) pdb=" O1 CLR D 503 " occ=0.75 Time building chain proxies: 3.85, per 1000 atoms: 0.23 Number of scatterers: 16997 At special positions: 0 Unit cell: (99.4542, 111.218, 164.688, 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) S 85 16.00 P 5 15.00 O 3138 8.00 N 2640 7.00 C 11129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 193 " distance=2.04 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 142 " distance=2.02 Simple disulfide: pdb=" SG CYS D 192 " - pdb=" SG CYS D 193 " distance=2.04 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 142 " 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 ALPHA1-6 " BMA F 3 " - " MAN F 4 " " MAN F 4 " - " MAN F 5 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " MAN K 4 " - " MAN K 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " NAG-ASN " NAG B 601 " - " ASN B 70 " " NAG E 501 " - " ASN E 68 " " NAG F 1 " - " ASN A 141 " " NAG G 1 " - " ASN B 143 " " NAG H 1 " - " ASN B 208 " " NAG I 1 " - " ASN C 141 " " NAG J 1 " - " ASN D 141 " " NAG K 1 " - " ASN E 141 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 628.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3894 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 20 sheets defined 43.7% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 1 through 12 Processing helix chain 'A' and resid 63 through 66 removed outlier: 3.563A pdb=" N ARG A 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 68 through 73 removed outlier: 4.232A pdb=" N GLY A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 212 through 218 Processing helix chain 'A' and resid 218 through 235 removed outlier: 4.053A pdb=" N THR A 229 " --> pdb=" O PHE A 225 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU A 231 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 233 " --> pdb=" O THR A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 240 Processing helix chain 'A' and resid 241 through 262 Processing helix chain 'A' and resid 272 through 300 Processing helix chain 'A' and resid 309 through 317 removed outlier: 3.726A pdb=" N ILE A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 371 through 426 removed outlier: 3.507A pdb=" N ALA A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 13 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 232 through 246 removed outlier: 3.713A pdb=" N ALA B 243 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 250 through 254 removed outlier: 3.619A pdb=" N GLY B 254 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 276 Processing helix chain 'B' and resid 286 through 314 Processing helix chain 'B' and resid 323 through 332 removed outlier: 3.656A pdb=" N GLU B 332 " --> pdb=" O GLN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 removed outlier: 4.196A pdb=" N ARG B 336 " --> pdb=" O GLU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 478 removed outlier: 3.653A pdb=" N SER B 421 " --> pdb=" O ASP B 417 " (cutoff:3.500A) Proline residue: B 463 - end of helix removed outlier: 3.811A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 68 through 73 removed outlier: 4.091A pdb=" N GLU C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.532A pdb=" N VAL C 85 " --> pdb=" O SER C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 180 removed outlier: 3.900A pdb=" N PHE C 180 " --> pdb=" O LYS C 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 180' Processing helix chain 'C' and resid 217 through 238 removed outlier: 4.639A pdb=" N ILE C 226 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 239 through 241 No H-bonds generated for 'chain 'C' and resid 239 through 241' Processing helix chain 'C' and resid 242 through 246 Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 278 through 306 Processing helix chain 'C' and resid 315 through 324 removed outlier: 3.585A pdb=" N GLU C 324 " --> pdb=" O GLN C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 331 removed outlier: 4.163A pdb=" N PHE C 329 " --> pdb=" O THR C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 460 Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 63 through 66 Processing helix chain 'D' and resid 68 through 73 removed outlier: 4.037A pdb=" N GLY D 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 85 Processing helix chain 'D' and resid 211 through 218 Processing helix chain 'D' and resid 218 through 230 removed outlier: 4.006A pdb=" N GLY D 230 " --> pdb=" O SER D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 236 through 240 Processing helix chain 'D' and resid 241 through 262 removed outlier: 3.834A pdb=" N GLU D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 300 Processing helix chain 'D' and resid 309 through 317 Processing helix chain 'D' and resid 319 through 323 Processing helix chain 'D' and resid 371 through 426 removed outlier: 3.613A pdb=" N PHE D 426 " --> pdb=" O THR D 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 13 removed outlier: 4.180A pdb=" N ARG E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 73 removed outlier: 3.993A pdb=" N GLU E 73 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 85 No H-bonds generated for 'chain 'E' and resid 83 through 85' Processing helix chain 'E' and resid 219 through 226 Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 236 through 243 Processing helix chain 'E' and resid 250 through 271 removed outlier: 3.628A pdb=" N GLN E 271 " --> pdb=" O PHE E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 309 Processing helix chain 'E' and resid 318 through 328 removed outlier: 3.615A pdb=" N PHE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 472 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.130A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 81 removed outlier: 4.130A pdb=" N LYS A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE A 49 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 43 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLU A 51 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ARG A 55 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LEU A 37 " --> pdb=" O ARG A 55 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG A 57 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU A 35 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N GLN A 59 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL A 33 " --> pdb=" O GLN A 59 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ILE A 61 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE A 31 " --> pdb=" O ILE A 61 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 removed outlier: 3.716A pdb=" N CYS A 142 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE A 148 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU A 199 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN A 208 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N MET A 178 " --> pdb=" O GLN A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 82 removed outlier: 4.602A pdb=" N GLY B 116 " --> pdb=" O ASP B 64 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 123 through 129 removed outlier: 6.808A pdb=" N THR B 51 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N SER B 44 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR B 53 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU B 42 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN B 55 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N TYR B 63 " --> pdb=" O ASN B 32 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASN B 32 " --> pdb=" O TYR B 63 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ILE B 178 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LEU B 37 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE B 220 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 92 through 94 removed outlier: 4.686A pdb=" N ALA B 150 " --> pdb=" O GLN B 213 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N GLN B 213 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AA9, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.868A pdb=" N ALA C 115 " --> pdb=" O GLN C 111 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 55 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 38 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 57 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR C 36 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY C 34 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 61 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ARG C 32 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL C 29 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N GLN C 159 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 31 " --> pdb=" O GLN C 159 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 121 through 127 removed outlier: 6.807A pdb=" N ASN C 53 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU C 40 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE C 55 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N THR C 38 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C 57 " --> pdb=" O THR C 36 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N THR C 36 " --> pdb=" O ASN C 57 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ALA C 59 " --> pdb=" O GLY C 34 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N GLY C 34 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR C 61 " --> pdb=" O ARG C 32 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N ARG C 32 " --> pdb=" O THR C 61 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N VAL C 174 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU C 35 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.150A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 212 " --> pdb=" O GLU C 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 90 through 92 removed outlier: 5.150A pdb=" N SER C 148 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU C 205 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N TYR C 204 " --> pdb=" O ARG C 198 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG C 198 " --> pdb=" O TYR C 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.216A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 4.216A pdb=" N LYS D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE D 49 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N VAL D 43 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU D 51 " --> pdb=" O ILE D 41 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ARG D 55 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N LEU D 37 " --> pdb=" O ARG D 55 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ARG D 57 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU D 35 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLN D 59 " --> pdb=" O VAL D 33 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL D 33 " --> pdb=" O GLN D 59 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N ILE D 61 " --> pdb=" O ILE D 31 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE D 31 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 90 through 92 removed outlier: 3.772A pdb=" N CYS D 142 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE D 148 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU D 199 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR D 198 " --> pdb=" O TRP D 187 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP D 187 " --> pdb=" O TYR D 198 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP D 200 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS D 185 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR D 202 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY D 183 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS D 204 " --> pdb=" O TYR D 181 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR D 181 " --> pdb=" O HIS D 204 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE D 206 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 77 through 81 removed outlier: 3.822A pdb=" N SER E 115 " --> pdb=" O TYR E 111 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLY E 114 " --> pdb=" O ASP E 62 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA E 49 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N SER E 42 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR E 51 " --> pdb=" O LEU E 40 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N LEU E 40 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASN E 53 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN E 61 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ASP E 30 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE E 29 " --> pdb=" O ASN E 157 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN E 159 " --> pdb=" O ILE E 29 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N VAL E 31 " --> pdb=" O GLN E 159 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE E 214 " --> pdb=" O ARG E 187 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 90 through 92 removed outlier: 5.232A pdb=" N SER E 148 " --> pdb=" O GLN E 207 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N GLN E 207 " --> pdb=" O SER E 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 162 through 163 921 hydrogen bonds defined for protein. 2646 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.46 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2644 1.31 - 1.44: 4786 1.44 - 1.58: 9853 1.58 - 1.71: 13 1.71 - 1.84: 139 Bond restraints: 17435 Sorted by residual: bond pdb=" C31 POV B 602 " pdb=" O31 POV B 602 " ideal model delta sigma weight residual 1.327 1.402 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C31 POV C 503 " pdb=" O31 POV C 503 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 POV C 502 " pdb=" O31 POV C 502 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C21 POV C 503 " pdb=" O21 POV C 503 " ideal model delta sigma weight residual 1.330 1.401 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C21 POV B 602 " pdb=" O21 POV B 602 " ideal model delta sigma weight residual 1.330 1.400 -0.070 2.00e-02 2.50e+03 1.24e+01 ... (remaining 17430 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 23384 2.62 - 5.25: 328 5.25 - 7.87: 47 7.87 - 10.50: 12 10.50 - 13.12: 10 Bond angle restraints: 23781 Sorted by residual: angle pdb=" O11 POV E 502 " pdb=" P POV E 502 " pdb=" O12 POV E 502 " ideal model delta sigma weight residual 97.67 110.79 -13.12 3.00e+00 1.11e-01 1.91e+01 angle pdb=" O11 POV C 502 " pdb=" P POV C 502 " pdb=" O12 POV C 502 " ideal model delta sigma weight residual 97.67 109.91 -12.24 3.00e+00 1.11e-01 1.66e+01 angle pdb=" O13 POV C 502 " pdb=" P POV C 502 " pdb=" O14 POV C 502 " ideal model delta sigma weight residual 121.11 109.06 12.05 3.00e+00 1.11e-01 1.61e+01 angle pdb=" O11 POV C 503 " pdb=" P POV C 503 " pdb=" O12 POV C 503 " ideal model delta sigma weight residual 97.67 109.61 -11.94 3.00e+00 1.11e-01 1.58e+01 angle pdb=" O11 POV B 602 " pdb=" P POV B 602 " pdb=" O12 POV B 602 " ideal model delta sigma weight residual 97.67 109.52 -11.85 3.00e+00 1.11e-01 1.56e+01 ... (remaining 23776 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 10485 29.83 - 59.67: 281 59.67 - 89.50: 67 89.50 - 119.34: 20 119.34 - 149.17: 2 Dihedral angle restraints: 10855 sinusoidal: 4875 harmonic: 5980 Sorted by residual: dihedral pdb=" CA CYS D 192 " pdb=" C CYS D 192 " pdb=" N CYS D 193 " pdb=" CA CYS D 193 " ideal model delta harmonic sigma weight residual -180.00 -150.93 -29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA GLU B 418 " pdb=" C GLU B 418 " pdb=" N ILE B 419 " pdb=" CA ILE B 419 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA CYS A 142 " pdb=" C CYS A 142 " pdb=" N THR A 143 " pdb=" CA THR A 143 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 10852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2353 0.059 - 0.118: 409 0.118 - 0.176: 44 0.176 - 0.235: 2 0.235 - 0.294: 7 Chirality restraints: 2815 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.57 0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C5 BMA I 3 " pdb=" C4 BMA I 3 " pdb=" C6 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2812 not shown) Planarity restraints: 2881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 483 " 0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO E 484 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO E 484 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 484 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 223 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.95e+00 pdb=" C ILE E 223 " -0.038 2.00e-02 2.50e+03 pdb=" O ILE E 223 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE E 224 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 393 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.78e+00 pdb=" C SER A 393 " -0.034 2.00e-02 2.50e+03 pdb=" O SER A 393 " 0.013 2.00e-02 2.50e+03 pdb=" N ASN A 394 " 0.011 2.00e-02 2.50e+03 ... (remaining 2878 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 91 2.51 - 3.10: 12885 3.10 - 3.70: 26834 3.70 - 4.30: 40888 4.30 - 4.90: 67704 Nonbonded interactions: 148402 Sorted by model distance: nonbonded pdb=" OG SER B 244 " pdb=" OG1 THR B 462 " model vdw 1.907 3.040 nonbonded pdb=" OD1 ASN B 98 " pdb=" OG SER B 129 " model vdw 2.032 3.040 nonbonded pdb=" OD2 ASP A 152 " pdb=" OG1 THR A 154 " model vdw 2.070 3.040 nonbonded pdb=" OG SER A 82 " pdb=" O THR A 106 " model vdw 2.085 3.040 nonbonded pdb=" OD2 ASP D 138 " pdb=" NE2 GLN D 140 " model vdw 2.107 3.120 ... (remaining 148397 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 1 through 501) selection = (chain 'D' and (resid 1 through 330 or resid 370 through 501)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' } 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=0.75 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: 1.460 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.020 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 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 0.075 17468 Z= 0.316 Angle : 0.812 13.119 23873 Z= 0.371 Chirality : 0.047 0.294 2815 Planarity : 0.004 0.056 2873 Dihedral : 15.710 149.173 6940 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.31 (0.19), residues: 1995 helix: 1.84 (0.19), residues: 756 sheet: -0.92 (0.24), residues: 389 loop : -0.68 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 147 TYR 0.015 0.002 TYR C 223 PHE 0.015 0.002 PHE C 12 TRP 0.014 0.002 TRP D 118 HIS 0.004 0.001 HIS B 103 Details of bonding type rmsd covalent geometry : bond 0.00676 (17435) covalent geometry : angle 0.80174 (23781) SS BOND : bond 0.00769 ( 7) SS BOND : angle 2.11828 ( 14) hydrogen bonds : bond 0.12008 ( 846) hydrogen bonds : angle 6.10941 ( 2646) link_ALPHA1-6 : bond 0.00556 ( 7) link_ALPHA1-6 : angle 1.77668 ( 21) link_BETA1-4 : bond 0.00572 ( 11) link_BETA1-4 : angle 2.01627 ( 33) link_NAG-ASN : bond 0.00940 ( 8) link_NAG-ASN : angle 2.83956 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.6454 time to fit residues: 64.9761 Evaluate side-chains 74 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 HIS B 276 GLN D 204 HIS D 385 HIS E 172 HIS ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN E 437 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.049960 restraints weight = 39283.739| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 2.82 r_work: 0.2570 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17468 Z= 0.157 Angle : 0.571 6.692 23873 Z= 0.286 Chirality : 0.044 0.172 2815 Planarity : 0.004 0.037 2873 Dihedral : 12.048 129.804 3031 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.91 % Allowed : 4.56 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 0.78 (0.19), residues: 1995 helix: 2.33 (0.18), residues: 767 sheet: -0.77 (0.24), residues: 388 loop : -0.51 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 168 TYR 0.015 0.001 TYR E 117 PHE 0.013 0.001 PHE E 467 TRP 0.011 0.001 TRP A 187 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00355 (17435) covalent geometry : angle 0.55790 (23781) SS BOND : bond 0.00736 ( 7) SS BOND : angle 1.88231 ( 14) hydrogen bonds : bond 0.04199 ( 846) hydrogen bonds : angle 4.52148 ( 2646) link_ALPHA1-6 : bond 0.00834 ( 7) link_ALPHA1-6 : angle 1.92277 ( 21) link_BETA1-4 : bond 0.00493 ( 11) link_BETA1-4 : angle 2.01828 ( 33) link_NAG-ASN : bond 0.00249 ( 8) link_NAG-ASN : angle 2.23365 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ASP cc_start: 0.8093 (t0) cc_final: 0.7477 (t0) REVERT: A 373 LYS cc_start: 0.6736 (mmtt) cc_final: 0.6478 (mmtt) REVERT: C 168 ARG cc_start: 0.8803 (ptp-110) cc_final: 0.8318 (ptm-80) REVERT: D 171 MET cc_start: 0.8132 (mtp) cc_final: 0.7679 (ptp) REVERT: D 208 GLN cc_start: 0.8688 (tp40) cc_final: 0.8459 (tp40) REVERT: D 324 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.7779 (mtp) REVERT: E 116 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8790 (mmm) outliers start: 17 outliers final: 6 residues processed: 88 average time/residue: 0.6331 time to fit residues: 62.0838 Evaluate side-chains 81 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 324 MET Chi-restraints excluded: chain D residue 418 CYS Chi-restraints excluded: chain E residue 116 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 141 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 126 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 20 HIS B 276 GLN D 3 HIS D 48 GLN D 310 GLN D 322 ASN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.049795 restraints weight = 39698.874| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 2.82 r_work: 0.2569 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17468 Z= 0.154 Angle : 0.518 7.326 23873 Z= 0.257 Chirality : 0.043 0.169 2815 Planarity : 0.003 0.037 2873 Dihedral : 10.100 126.860 3031 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.18 % Allowed : 5.80 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.01 (0.19), residues: 1995 helix: 2.60 (0.18), residues: 771 sheet: -0.75 (0.24), residues: 389 loop : -0.42 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 20 TYR 0.012 0.001 TYR B 439 PHE 0.013 0.001 PHE E 467 TRP 0.010 0.001 TRP A 67 HIS 0.003 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00350 (17435) covalent geometry : angle 0.50423 (23781) SS BOND : bond 0.00602 ( 7) SS BOND : angle 1.97467 ( 14) hydrogen bonds : bond 0.03859 ( 846) hydrogen bonds : angle 4.18353 ( 2646) link_ALPHA1-6 : bond 0.00700 ( 7) link_ALPHA1-6 : angle 1.89285 ( 21) link_BETA1-4 : bond 0.00447 ( 11) link_BETA1-4 : angle 1.92900 ( 33) link_NAG-ASN : bond 0.00196 ( 8) link_NAG-ASN : angle 2.01975 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.671 Fit side-chains REVERT: A 373 LYS cc_start: 0.6733 (mmtt) cc_final: 0.6484 (mmtt) REVERT: C 168 ARG cc_start: 0.8797 (ptp-110) cc_final: 0.8282 (ptm-80) REVERT: D 117 MET cc_start: 0.8977 (tpt) cc_final: 0.8645 (tpt) REVERT: D 171 MET cc_start: 0.8065 (mtp) cc_final: 0.7625 (ptp) REVERT: D 208 GLN cc_start: 0.8679 (tp40) cc_final: 0.8475 (tp40) REVERT: E 116 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8818 (mmm) outliers start: 22 outliers final: 5 residues processed: 88 average time/residue: 0.5652 time to fit residues: 55.7433 Evaluate side-chains 79 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 146 optimal weight: 0.1980 chunk 45 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.064901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.049372 restraints weight = 39711.737| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.81 r_work: 0.2560 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2568 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2568 r_free = 0.2568 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17468 Z= 0.168 Angle : 0.519 7.710 23873 Z= 0.258 Chirality : 0.043 0.196 2815 Planarity : 0.003 0.034 2873 Dihedral : 9.389 124.506 3031 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.56 % Allowed : 6.44 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % 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 aren not related in a simple way. whole: 1.13 (0.19), residues: 1995 helix: 2.71 (0.18), residues: 771 sheet: -0.69 (0.24), residues: 387 loop : -0.37 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 499 TYR 0.013 0.001 TYR B 439 PHE 0.012 0.001 PHE E 467 TRP 0.010 0.001 TRP A 311 HIS 0.004 0.001 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00386 (17435) covalent geometry : angle 0.50627 (23781) SS BOND : bond 0.00825 ( 7) SS BOND : angle 1.98475 ( 14) hydrogen bonds : bond 0.03726 ( 846) hydrogen bonds : angle 4.08299 ( 2646) link_ALPHA1-6 : bond 0.00740 ( 7) link_ALPHA1-6 : angle 1.88677 ( 21) link_BETA1-4 : bond 0.00367 ( 11) link_BETA1-4 : angle 1.82941 ( 33) link_NAG-ASN : bond 0.00259 ( 8) link_NAG-ASN : angle 1.96664 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.598 Fit side-chains REVERT: A 373 LYS cc_start: 0.6597 (mmtt) cc_final: 0.6273 (mmtt) REVERT: A 397 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8383 (mp0) REVERT: C 436 ASP cc_start: 0.8227 (t0) cc_final: 0.8000 (t0) REVERT: D 171 MET cc_start: 0.8016 (mtp) cc_final: 0.7630 (ptp) REVERT: D 208 GLN cc_start: 0.8692 (tp40) cc_final: 0.8425 (tp40) REVERT: D 324 MET cc_start: 0.9098 (mpp) cc_final: 0.8810 (mtp) REVERT: E 116 MET cc_start: 0.9233 (OUTLIER) cc_final: 0.8829 (mmm) outliers start: 29 outliers final: 8 residues processed: 97 average time/residue: 0.5822 time to fit residues: 63.2807 Evaluate side-chains 88 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 63 optimal weight: 6.9990 chunk 22 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 192 optimal weight: 7.9990 chunk 180 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 GLN B 276 GLN B 437 ASN D 310 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.065906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.050458 restraints weight = 39217.740| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.80 r_work: 0.2602 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 17468 Z= 0.122 Angle : 0.519 16.865 23873 Z= 0.255 Chirality : 0.042 0.181 2815 Planarity : 0.003 0.039 2873 Dihedral : 9.060 123.316 3031 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.56 % Allowed : 7.14 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.22 (0.19), residues: 1995 helix: 2.73 (0.18), residues: 778 sheet: -0.69 (0.24), residues: 392 loop : -0.26 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 168 TYR 0.012 0.001 TYR B 439 PHE 0.012 0.001 PHE E 467 TRP 0.010 0.001 TRP A 311 HIS 0.004 0.000 HIS B 60 Details of bonding type rmsd covalent geometry : bond 0.00277 (17435) covalent geometry : angle 0.50393 (23781) SS BOND : bond 0.00648 ( 7) SS BOND : angle 3.17225 ( 14) hydrogen bonds : bond 0.03542 ( 846) hydrogen bonds : angle 3.96500 ( 2646) link_ALPHA1-6 : bond 0.00750 ( 7) link_ALPHA1-6 : angle 1.76415 ( 21) link_BETA1-4 : bond 0.00455 ( 11) link_BETA1-4 : angle 1.66475 ( 33) link_NAG-ASN : bond 0.00111 ( 8) link_NAG-ASN : angle 1.84746 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 83 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 373 LYS cc_start: 0.6626 (mmtt) cc_final: 0.6244 (mmtt) REVERT: C 168 ARG cc_start: 0.8743 (ptp-110) cc_final: 0.8324 (ptm-80) REVERT: C 436 ASP cc_start: 0.8234 (t0) cc_final: 0.8001 (t0) REVERT: D 48 GLN cc_start: 0.9085 (mt0) cc_final: 0.8730 (mt0) REVERT: D 171 MET cc_start: 0.7922 (mtp) cc_final: 0.7541 (ptp) REVERT: D 208 GLN cc_start: 0.8688 (tp40) cc_final: 0.8431 (tp40) REVERT: D 324 MET cc_start: 0.9101 (mpp) cc_final: 0.8845 (mtp) REVERT: E 116 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8804 (mmm) outliers start: 29 outliers final: 11 residues processed: 102 average time/residue: 0.5836 time to fit residues: 66.4900 Evaluate side-chains 91 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 148 optimal weight: 0.6980 chunk 113 optimal weight: 9.9990 chunk 196 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 76 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 22 optimal weight: 0.3980 chunk 125 optimal weight: 3.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 HIS B 276 GLN ** E 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.065165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.049689 restraints weight = 39239.077| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.79 r_work: 0.2581 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17468 Z= 0.160 Angle : 0.530 16.042 23873 Z= 0.260 Chirality : 0.042 0.187 2815 Planarity : 0.003 0.035 2873 Dihedral : 8.858 122.923 3031 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.45 % Allowed : 7.89 % Favored : 90.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.24 (0.19), residues: 1995 helix: 2.77 (0.18), residues: 777 sheet: -0.67 (0.24), residues: 397 loop : -0.27 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 168 TYR 0.013 0.001 TYR B 439 PHE 0.012 0.001 PHE E 467 TRP 0.009 0.001 TRP A 311 HIS 0.005 0.001 HIS A 408 Details of bonding type rmsd covalent geometry : bond 0.00369 (17435) covalent geometry : angle 0.51380 (23781) SS BOND : bond 0.01032 ( 7) SS BOND : angle 3.42132 ( 14) hydrogen bonds : bond 0.03573 ( 846) hydrogen bonds : angle 3.95749 ( 2646) link_ALPHA1-6 : bond 0.00699 ( 7) link_ALPHA1-6 : angle 1.79129 ( 21) link_BETA1-4 : bond 0.00388 ( 11) link_BETA1-4 : angle 1.74949 ( 33) link_NAG-ASN : bond 0.00241 ( 8) link_NAG-ASN : angle 1.88580 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3990 Ramachandran restraints generated. 1995 Oldfield, 0 Emsley, 1995 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 282 MET cc_start: 0.8508 (ttm) cc_final: 0.8266 (mtp) REVERT: A 373 LYS cc_start: 0.6611 (mmtt) cc_final: 0.6157 (mmtt) REVERT: A 397 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8325 (mp0) REVERT: C 168 ARG cc_start: 0.8747 (ptp-110) cc_final: 0.8310 (ptm-80) REVERT: C 436 ASP cc_start: 0.8237 (t0) cc_final: 0.7986 (t0) REVERT: D 48 GLN cc_start: 0.9069 (mt0) cc_final: 0.8747 (mt0) REVERT: D 171 MET cc_start: 0.7925 (mtp) cc_final: 0.7525 (ptp) REVERT: D 208 GLN cc_start: 0.8686 (tp40) cc_final: 0.8423 (tp40) REVERT: D 324 MET cc_start: 0.9112 (mpp) cc_final: 0.8863 (mtp) REVERT: D 407 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: E 116 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8832 (mmm) outliers start: 27 outliers final: 13 residues processed: 99 average time/residue: 0.5674 time to fit residues: 62.8397 Evaluate side-chains 94 residues out of total 1863 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 193 CYS Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 282 MET Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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: 72.4782 > 50: distance: 69 - 73: 28.576 distance: 73 - 74: 58.354 distance: 73 - 189: 27.927 distance: 74 - 75: 19.047 distance: 74 - 77: 8.419 distance: 75 - 76: 9.151 distance: 75 - 81: 48.872 distance: 76 - 186: 27.133 distance: 77 - 78: 56.443 distance: 78 - 79: 40.658 distance: 78 - 80: 39.266 distance: 81 - 82: 39.184 distance: 81 - 87: 56.716 distance: 82 - 83: 43.412 distance: 82 - 85: 38.650 distance: 83 - 84: 16.163 distance: 83 - 88: 15.982 distance: 84 - 102: 39.993 distance: 86 - 87: 56.396 distance: 88 - 89: 40.201 distance: 89 - 90: 40.517 distance: 89 - 92: 56.119 distance: 90 - 91: 56.340 distance: 90 - 94: 40.858 distance: 91 - 110: 56.436 distance: 92 - 93: 23.454 distance: 95 - 96: 43.938 distance: 95 - 98: 57.387 distance: 96 - 97: 43.519 distance: 96 - 102: 45.706 distance: 98 - 99: 66.268 distance: 99 - 100: 19.413 distance: 99 - 101: 55.981 distance: 103 - 104: 47.788 distance: 103 - 106: 39.312 distance: 104 - 105: 14.957 distance: 104 - 110: 36.340 distance: 106 - 107: 39.115 distance: 107 - 109: 18.044 distance: 110 - 111: 11.807 distance: 111 - 112: 62.098 distance: 111 - 114: 64.536 distance: 112 - 117: 26.526 distance: 114 - 115: 38.740 distance: 117 - 118: 23.359 distance: 118 - 119: 39.733 distance: 118 - 121: 54.224 distance: 119 - 120: 56.134 distance: 123 - 125: 68.784 distance: 124 - 126: 57.208 distance: 125 - 126: 30.817 distance: 126 - 128: 34.938 distance: 127 - 129: 11.861 distance: 129 - 130: 63.925 distance: 132 - 133: 51.043 distance: 132 - 135: 40.726 distance: 133 - 134: 52.203 distance: 133 - 139: 42.098 distance: 135 - 136: 55.323 distance: 136 - 137: 57.773 distance: 136 - 138: 39.506 distance: 139 - 140: 35.767 distance: 139 - 145: 47.972 distance: 140 - 141: 36.721 distance: 140 - 143: 40.604 distance: 141 - 142: 36.683 distance: 141 - 146: 23.006 distance: 143 - 144: 35.175 distance: 144 - 145: 34.409 distance: 146 - 147: 13.451 distance: 147 - 148: 56.346 distance: 148 - 149: 57.503 distance: 148 - 154: 33.602 distance: 150 - 151: 35.651 distance: 151 - 152: 41.050 distance: 151 - 153: 29.306