Starting phenix.real_space_refine on Sun Jul 5 14:26:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdb_45466/07_2026/9cdb_45466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdb_45466/07_2026/9cdb_45466.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9cdb_45466/07_2026/9cdb_45466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdb_45466/07_2026/9cdb_45466.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cdb_45466/07_2026/9cdb_45466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdb_45466/07_2026/9cdb_45466.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.021 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 6 5.21 5 S 162 5.16 5 C 18094 2.51 5 N 4931 2.21 5 O 5376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28605 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "B" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 572} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "D" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 572} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 4666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4666 Classifications: {'peptide': 592} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 564} Chain breaks: 1 Chain: "F" Number of atoms: 4720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4720 Classifications: {'peptide': 600} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 572} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 3, 56 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 1} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 3, 56 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 56 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 3, 56 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' A%rna3p_pur:plan': 1, ' A%rna3p_pur:plan2': 1} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ATP:plan-1': 1, 'ATP:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 24 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ATP:plan-1': 1, 'ATP:plan-2': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 4 Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 9 residue: pdb=" P A A H 2 " occ=0.69 ... (20 atoms not shown) pdb=" C4 A A H 2 " occ=0.69 residue: pdb=" P A A H 3 " occ=0.68 ... (10 atoms not shown) pdb=" C1'A A H 3 " occ=0.68 residue: pdb=" P A A H 4 " occ=0.65 ... (20 atoms not shown) pdb=" C4 A A H 4 " occ=0.65 residue: pdb=" P A A I 5 " occ=0.72 ... (20 atoms not shown) pdb=" C4 A A I 5 " occ=0.72 residue: pdb=" P A A I 6 " occ=0.70 ... (10 atoms not shown) pdb=" C1'A A I 6 " occ=0.70 residue: pdb=" P A A I 7 " occ=0.72 ... (20 atoms not shown) pdb=" C4 A A I 7 " occ=0.72 residue: pdb=" P A A J 8 " occ=0.56 ... (20 atoms not shown) pdb=" C4 A A J 8 " occ=0.56 residue: pdb=" P A A J 9 " occ=0.70 ... (10 atoms not shown) pdb=" C1'A A J 9 " occ=0.70 residue: pdb=" P A A J 10 " occ=0.65 ... (20 atoms not shown) pdb=" C4 A A J 10 " occ=0.65 Time building chain proxies: 5.58, per 1000 atoms: 0.20 Number of scatterers: 28605 At special positions: 0 Unit cell: (105.17, 203.868, 198.205, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 162 16.00 P 36 15.00 Mg 6 11.99 O 5376 8.00 N 4931 7.00 C 18094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 997.0 milliseconds 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6732 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 13 sheets defined 53.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 14 through 23 removed outlier: 3.717A pdb=" N GLU A 18 " --> pdb=" O MET A 14 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 23 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 50 removed outlier: 4.233A pdb=" N LEU A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 161 through 167 removed outlier: 3.694A pdb=" N LYS A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 208 through 214 Processing helix chain 'A' and resid 215 through 224 Processing helix chain 'A' and resid 230 through 237 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.843A pdb=" N GLY A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 335 through 339 Processing helix chain 'A' and resid 347 through 369 Processing helix chain 'A' and resid 390 through 405 removed outlier: 3.737A pdb=" N GLN A 405 " --> pdb=" O ILE A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 430 removed outlier: 6.789A pdb=" N ALA A 428 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N SER A 429 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 430 " --> pdb=" O ARG A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 442 removed outlier: 4.552A pdb=" N ALA A 437 " --> pdb=" O HIS A 433 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 479 through 489 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 517 through 525 Processing helix chain 'A' and resid 534 through 539 removed outlier: 3.553A pdb=" N SER A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 548 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 557 through 572 Processing helix chain 'A' and resid 575 through 596 Processing helix chain 'B' and resid 15 through 23 removed outlier: 4.170A pdb=" N VAL B 23 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 51 removed outlier: 4.677A pdb=" N LEU B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 133 through 144 Processing helix chain 'B' and resid 157 through 163 Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 180 through 199 Processing helix chain 'B' and resid 215 through 224 Processing helix chain 'B' and resid 230 through 237 Processing helix chain 'B' and resid 252 through 262 removed outlier: 3.670A pdb=" N LEU B 256 " --> pdb=" O SER B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 307 through 325 Processing helix chain 'B' and resid 335 through 339 Processing helix chain 'B' and resid 341 through 345 Processing helix chain 'B' and resid 347 through 369 removed outlier: 3.754A pdb=" N LYS B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 405 removed outlier: 3.658A pdb=" N GLN B 405 " --> pdb=" O ILE B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 427 Processing helix chain 'B' and resid 431 through 442 removed outlier: 4.376A pdb=" N ALA B 437 " --> pdb=" O HIS B 433 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 496 through 504 Processing helix chain 'B' and resid 517 through 525 Processing helix chain 'B' and resid 534 through 539 Processing helix chain 'B' and resid 541 through 548 Processing helix chain 'B' and resid 548 through 553 Processing helix chain 'B' and resid 557 through 572 Processing helix chain 'B' and resid 575 through 600 Processing helix chain 'C' and resid 15 through 21 removed outlier: 3.527A pdb=" N ALA C 19 " --> pdb=" O VAL C 15 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 21 " --> pdb=" O PRO C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 51 removed outlier: 4.359A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER C 51 " --> pdb=" O ASP C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 87 removed outlier: 3.702A pdb=" N PHE C 76 " --> pdb=" O ARG C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 118 Processing helix chain 'C' and resid 133 through 144 removed outlier: 3.511A pdb=" N MET C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 167 removed outlier: 3.601A pdb=" N LYS C 165 " --> pdb=" O ARG C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 188 removed outlier: 4.118A pdb=" N GLU C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 214 Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 230 through 237 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 253 through 261 Processing helix chain 'C' and resid 289 through 298 Processing helix chain 'C' and resid 307 through 325 Processing helix chain 'C' and resid 335 through 340 removed outlier: 3.710A pdb=" N ALA C 340 " --> pdb=" O ASN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 345 removed outlier: 3.848A pdb=" N LYS C 344 " --> pdb=" O ASP C 341 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN C 345 " --> pdb=" O LYS C 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 345' Processing helix chain 'C' and resid 347 through 369 Processing helix chain 'C' and resid 390 through 404 removed outlier: 4.281A pdb=" N SER C 394 " --> pdb=" O LEU C 390 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET C 404 " --> pdb=" O ALA C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 423 through 427 Processing helix chain 'C' and resid 431 through 441 removed outlier: 4.176A pdb=" N LYS C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ALA C 437 " --> pdb=" O HIS C 433 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL C 438 " --> pdb=" O ASP C 434 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 473 through 478 removed outlier: 4.004A pdb=" N LEU C 476 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU C 477 " --> pdb=" O LEU C 474 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU C 478 " --> pdb=" O ASN C 475 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 478' Processing helix chain 'C' and resid 479 through 489 Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 517 through 525 Processing helix chain 'C' and resid 534 through 539 Processing helix chain 'C' and resid 541 through 548 Processing helix chain 'C' and resid 548 through 553 Processing helix chain 'C' and resid 557 through 572 Processing helix chain 'C' and resid 575 through 598 Processing helix chain 'D' and resid 12 through 14 No H-bonds generated for 'chain 'D' and resid 12 through 14' Processing helix chain 'D' and resid 15 through 23 removed outlier: 4.195A pdb=" N VAL D 23 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 4.446A pdb=" N LEU D 45 " --> pdb=" O ASN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 87 Processing helix chain 'D' and resid 103 through 118 Processing helix chain 'D' and resid 133 through 144 Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 180 through 199 removed outlier: 3.842A pdb=" N SER D 185 " --> pdb=" O LEU D 181 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 224 Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 230 through 237 removed outlier: 3.633A pdb=" N ASN D 236 " --> pdb=" O ALA D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 262 removed outlier: 3.610A pdb=" N LEU D 256 " --> pdb=" O SER D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 298 removed outlier: 3.627A pdb=" N GLY D 297 " --> pdb=" O TYR D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 325 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.661A pdb=" N TYR D 339 " --> pdb=" O SER D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 369 Processing helix chain 'D' and resid 391 through 405 removed outlier: 3.702A pdb=" N GLN D 405 " --> pdb=" O ILE D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 427 removed outlier: 3.604A pdb=" N ARG D 427 " --> pdb=" O LYS D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 441 removed outlier: 3.541A pdb=" N PHE D 435 " --> pdb=" O TYR D 431 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALA D 437 " --> pdb=" O HIS D 433 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL D 438 " --> pdb=" O ASP D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 464 Processing helix chain 'D' and resid 475 through 478 Processing helix chain 'D' and resid 479 through 490 Processing helix chain 'D' and resid 496 through 504 Processing helix chain 'D' and resid 517 through 525 Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 541 through 548 Processing helix chain 'D' and resid 548 through 553 Processing helix chain 'D' and resid 557 through 572 Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.629A pdb=" N LYS D 599 " --> pdb=" O LEU D 595 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 21 removed outlier: 4.130A pdb=" N ALA E 19 " --> pdb=" O VAL E 15 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N HIS E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 51 removed outlier: 3.700A pdb=" N SER E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 89 Processing helix chain 'E' and resid 103 through 118 Processing helix chain 'E' and resid 133 through 144 removed outlier: 3.574A pdb=" N MET E 137 " --> pdb=" O ASN E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 167 removed outlier: 3.562A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 188 removed outlier: 3.743A pdb=" N SER E 185 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 214 Processing helix chain 'E' and resid 215 through 224 Processing helix chain 'E' and resid 230 through 237 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 253 through 261 removed outlier: 3.968A pdb=" N ASP E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 269 Processing helix chain 'E' and resid 289 through 297 removed outlier: 3.685A pdb=" N GLY E 297 " --> pdb=" O TYR E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 325 Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 347 through 369 removed outlier: 3.513A pdb=" N LYS E 369 " --> pdb=" O GLU E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 404 removed outlier: 4.179A pdb=" N SER E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 407 No H-bonds generated for 'chain 'E' and resid 405 through 407' Processing helix chain 'E' and resid 434 through 441 removed outlier: 4.512A pdb=" N VAL E 438 " --> pdb=" O ASP E 434 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 464 Processing helix chain 'E' and resid 479 through 490 Processing helix chain 'E' and resid 496 through 504 Processing helix chain 'E' and resid 517 through 525 Processing helix chain 'E' and resid 534 through 539 Processing helix chain 'E' and resid 541 through 548 Processing helix chain 'E' and resid 548 through 553 Processing helix chain 'E' and resid 557 through 572 Processing helix chain 'E' and resid 575 through 596 Processing helix chain 'F' and resid 14 through 23 removed outlier: 3.827A pdb=" N VAL F 23 " --> pdb=" O ALA F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 51 Processing helix chain 'F' and resid 70 through 88 Processing helix chain 'F' and resid 103 through 118 Processing helix chain 'F' and resid 136 through 144 Processing helix chain 'F' and resid 157 through 162 Processing helix chain 'F' and resid 163 through 166 Processing helix chain 'F' and resid 180 through 199 removed outlier: 3.634A pdb=" N LEU F 190 " --> pdb=" O ILE F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 215 through 224 Processing helix chain 'F' and resid 227 through 229 No H-bonds generated for 'chain 'F' and resid 227 through 229' Processing helix chain 'F' and resid 230 through 237 Processing helix chain 'F' and resid 252 through 262 removed outlier: 3.885A pdb=" N LEU F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 297 removed outlier: 3.642A pdb=" N GLY F 297 " --> pdb=" O TYR F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 325 Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.866A pdb=" N TYR F 339 " --> pdb=" O SER F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 345 Processing helix chain 'F' and resid 347 through 369 removed outlier: 3.838A pdb=" N LYS F 369 " --> pdb=" O GLU F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 405 removed outlier: 4.228A pdb=" N SER F 394 " --> pdb=" O LEU F 390 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN F 405 " --> pdb=" O ILE F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 427 Processing helix chain 'F' and resid 429 through 434 removed outlier: 3.569A pdb=" N GLU F 432 " --> pdb=" O SER F 429 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N HIS F 433 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP F 434 " --> pdb=" O TYR F 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 429 through 434' Processing helix chain 'F' and resid 435 through 441 Processing helix chain 'F' and resid 454 through 464 Processing helix chain 'F' and resid 475 through 478 Processing helix chain 'F' and resid 479 through 489 Processing helix chain 'F' and resid 496 through 504 Processing helix chain 'F' and resid 517 through 525 Processing helix chain 'F' and resid 534 through 539 Processing helix chain 'F' and resid 541 through 553 removed outlier: 3.815A pdb=" N LEU F 549 " --> pdb=" O ASN F 545 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA F 550 " --> pdb=" O LEU F 546 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ASP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 572 Processing helix chain 'F' and resid 575 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 61 removed outlier: 6.184A pdb=" N VAL A 4 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N CYS A 98 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 6 " --> pdb=" O CYS A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 245 removed outlier: 5.923A pdb=" N LYS A 239 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 329 " --> pdb=" O LYS A 239 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N HIS A 243 " --> pdb=" O GLU A 331 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N ARG A 333 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N HIS A 245 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE A 413 " --> pdb=" O VAL A 376 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU A 378 " --> pdb=" O ILE A 413 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY A 415 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 419 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 445 " --> pdb=" O ARG A 469 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY A 471 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ALA A 447 " --> pdb=" O GLY A 471 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 470 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 62 removed outlier: 6.098A pdb=" N LEU B 5 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE B 33 " --> pdb=" O LEU B 5 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS B 7 " --> pdb=" O PHE B 33 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N THR B 35 " --> pdb=" O CYS B 7 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 4 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N CYS B 98 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 6 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 97 " --> pdb=" O PHE B 123 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL B 125 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN B 120 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR B 153 " --> pdb=" O GLN B 120 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 122 " --> pdb=" O MET B 151 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 239 through 245 removed outlier: 4.554A pdb=" N VAL B 240 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N GLU B 331 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LEU B 242 " --> pdb=" O GLU B 331 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 333 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N CYS B 244 " --> pdb=" O ARG B 333 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL B 414 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N LEU B 378 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N VAL B 416 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N VAL B 380 " --> pdb=" O VAL B 416 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU B 418 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL B 414 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR B 446 " --> pdb=" O VAL B 414 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL B 416 " --> pdb=" O THR B 446 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 445 " --> pdb=" O ARG B 469 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLY B 471 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N ALA B 447 " --> pdb=" O GLY B 471 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 57 through 61 removed outlier: 3.512A pdb=" N SER C 58 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU C 5 " --> pdb=" O HIS C 31 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N PHE C 33 " --> pdb=" O LEU C 5 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS C 7 " --> pdb=" O PHE C 33 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL C 4 " --> pdb=" O TYR C 96 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N CYS C 98 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 6 " --> pdb=" O CYS C 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 123 through 126 Processing sheet with id=AA7, first strand: chain 'C' and resid 239 through 245 removed outlier: 4.334A pdb=" N VAL C 240 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU C 331 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU C 242 " --> pdb=" O GLU C 331 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ARG C 333 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N CYS C 244 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ILE C 413 " --> pdb=" O VAL C 376 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU C 378 " --> pdb=" O ILE C 413 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY C 415 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA C 419 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL C 445 " --> pdb=" O ARG C 469 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLY C 471 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ALA C 447 " --> pdb=" O GLY C 471 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU C 470 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 493 " --> pdb=" O SER C 529 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 56 through 62 removed outlier: 3.600A pdb=" N VAL D 32 " --> pdb=" O SER D 58 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU D 5 " --> pdb=" O HIS D 31 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N PHE D 33 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS D 7 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR D 35 " --> pdb=" O CYS D 7 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL D 4 " --> pdb=" O TYR D 96 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N CYS D 98 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU D 6 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL D 97 " --> pdb=" O PHE D 123 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL D 125 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL D 122 " --> pdb=" O MET D 151 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 239 through 245 removed outlier: 7.595A pdb=" N LYS D 239 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ALA D 330 " --> pdb=" O LYS D 239 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP D 241 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE D 332 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N HIS D 243 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 10.000A pdb=" N CYS D 334 " --> pdb=" O HIS D 243 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N HIS D 245 " --> pdb=" O CYS D 334 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA D 328 " --> pdb=" O HIS D 375 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ASN D 377 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA D 330 " --> pdb=" O ASN D 377 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 379 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE D 332 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ILE D 381 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N CYS D 334 " --> pdb=" O ILE D 381 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N VAL D 414 " --> pdb=" O VAL D 376 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU D 378 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 416 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL D 380 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU D 418 " --> pdb=" O VAL D 380 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA D 444 " --> pdb=" O VAL D 414 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL D 445 " --> pdb=" O ARG D 469 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLY D 471 " --> pdb=" O VAL D 445 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ALA D 447 " --> pdb=" O GLY D 471 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU D 470 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 56 through 62 removed outlier: 3.634A pdb=" N SER E 58 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU E 5 " --> pdb=" O HIS E 31 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N PHE E 33 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N CYS E 7 " --> pdb=" O PHE E 33 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR E 35 " --> pdb=" O CYS E 7 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL E 4 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS E 98 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 6 " --> pdb=" O CYS E 98 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL E 97 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL E 125 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLN E 120 " --> pdb=" O TYR E 153 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TYR E 153 " --> pdb=" O GLN E 120 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E 122 " --> pdb=" O MET E 151 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 126 " --> pdb=" O HIS E 147 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N HIS E 147 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 239 through 245 removed outlier: 5.854A pdb=" N LYS E 239 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR E 329 " --> pdb=" O LYS E 239 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N HIS E 243 " --> pdb=" O GLU E 331 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ARG E 333 " --> pdb=" O HIS E 243 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N HIS E 245 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA E 328 " --> pdb=" O HIS E 375 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N ASN E 377 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA E 330 " --> pdb=" O ASN E 377 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU E 379 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE E 332 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N ILE E 381 " --> pdb=" O ILE E 332 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N CYS E 334 " --> pdb=" O ILE E 381 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL E 414 " --> pdb=" O VAL E 376 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU E 378 " --> pdb=" O VAL E 414 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL E 416 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N VAL E 380 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU E 418 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL E 445 " --> pdb=" O ARG E 469 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLY E 471 " --> pdb=" O VAL E 445 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ALA E 447 " --> pdb=" O GLY E 471 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 470 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 56 through 62 removed outlier: 3.660A pdb=" N SER F 58 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL F 32 " --> pdb=" O SER F 58 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU F 5 " --> pdb=" O HIS F 31 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N PHE F 33 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N CYS F 7 " --> pdb=" O PHE F 33 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N THR F 35 " --> pdb=" O CYS F 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU F 6 " --> pdb=" O CYS F 98 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL F 97 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL F 125 " --> pdb=" O VAL F 97 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER F 121 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLY F 152 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N PHE F 123 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU F 150 " --> pdb=" O PHE F 123 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL F 125 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N PHE F 148 " --> pdb=" O VAL F 125 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 239 through 245 removed outlier: 6.073A pdb=" N LYS F 239 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N TYR F 329 " --> pdb=" O LYS F 239 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N HIS F 243 " --> pdb=" O GLU F 331 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG F 333 " --> pdb=" O HIS F 243 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N HIS F 245 " --> pdb=" O ARG F 333 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA F 328 " --> pdb=" O HIS F 375 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ASN F 377 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ALA F 330 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU F 379 " --> pdb=" O ALA F 330 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE F 332 " --> pdb=" O LEU F 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE F 381 " --> pdb=" O ILE F 332 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N CYS F 334 " --> pdb=" O ILE F 381 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N VAL F 414 " --> pdb=" O VAL F 376 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU F 378 " --> pdb=" O VAL F 414 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N VAL F 416 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL F 380 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU F 418 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS F 448 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 469 " --> pdb=" O VAL F 445 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU F 470 " --> pdb=" O GLU F 494 " (cutoff:3.500A) 1284 hydrogen bonds defined for protein. 3696 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: 5.23 Time building geometry restraints manager: 2.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9433 1.35 - 1.46: 6581 1.46 - 1.58: 12927 1.58 - 1.70: 69 1.70 - 1.82: 246 Bond restraints: 29256 Sorted by residual: bond pdb=" C1' ATP F 701 " pdb=" C2' ATP F 701 " ideal model delta sigma weight residual 1.531 1.298 0.233 1.20e-02 6.94e+03 3.78e+02 bond pdb=" C1' ATP B 701 " pdb=" C2' ATP B 701 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.69e+02 bond pdb=" C1' ATP F 702 " pdb=" C2' ATP F 702 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.59e+02 bond pdb=" C1' ATP D 701 " pdb=" C2' ATP D 701 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.59e+02 bond pdb=" C1' ATP B 702 " pdb=" C2' ATP B 702 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.58e+02 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 39405 3.38 - 6.75: 231 6.75 - 10.13: 66 10.13 - 13.50: 12 13.50 - 16.88: 8 Bond angle restraints: 39722 Sorted by residual: angle pdb=" PB ATP D 702 " pdb=" O3B ATP D 702 " pdb=" PG ATP D 702 " ideal model delta sigma weight residual 139.87 122.99 16.88 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 123.19 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" PB ATP B 702 " pdb=" O3B ATP B 702 " pdb=" PG ATP B 702 " ideal model delta sigma weight residual 139.87 123.22 16.65 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 123.23 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.41 16.46 1.00e+00 1.00e+00 2.71e+02 ... (remaining 39717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14782 17.89 - 35.77: 2108 35.77 - 53.66: 614 53.66 - 71.55: 136 71.55 - 89.43: 62 Dihedral angle restraints: 17702 sinusoidal: 7301 harmonic: 10401 Sorted by residual: dihedral pdb=" CD ARG F 588 " pdb=" NE ARG F 588 " pdb=" CZ ARG F 588 " pdb=" NH1 ARG F 588 " ideal model delta sinusoidal sigma weight residual 0.00 -48.79 48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA LEU B 211 " pdb=" C LEU B 211 " pdb=" N ALA B 212 " pdb=" CA ALA B 212 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CD ARG B 588 " pdb=" NE ARG B 588 " pdb=" CZ ARG B 588 " pdb=" NH1 ARG B 588 " ideal model delta sinusoidal sigma weight residual 0.00 42.80 -42.80 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 17699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3814 0.061 - 0.122: 550 0.122 - 0.184: 21 0.184 - 0.245: 3 0.245 - 0.306: 8 Chirality restraints: 4396 Sorted by residual: chirality pdb=" C2' ATP D 701 " pdb=" C1' ATP D 701 " pdb=" C3' ATP D 701 " pdb=" O2' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' ATP E 702 " pdb=" C1' ATP E 702 " pdb=" C3' ATP E 702 " pdb=" O2' ATP E 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C2' ATP B 702 " pdb=" C1' ATP B 702 " pdb=" C3' ATP B 702 " pdb=" O2' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4393 not shown) Planarity restraints: 5077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 588 " -0.814 9.50e-02 1.11e+02 3.65e-01 8.09e+01 pdb=" NE ARG F 588 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG F 588 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 588 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 588 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 588 " 0.741 9.50e-02 1.11e+02 3.32e-01 6.72e+01 pdb=" NE ARG B 588 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG B 588 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 588 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 588 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 588 " 0.667 9.50e-02 1.11e+02 2.99e-01 5.44e+01 pdb=" NE ARG D 588 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG D 588 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 588 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 588 " 0.021 2.00e-02 2.50e+03 ... (remaining 5074 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 321 2.56 - 3.14: 23164 3.14 - 3.73: 48888 3.73 - 4.31: 61824 4.31 - 4.90: 104332 Nonbonded interactions: 238529 Sorted by model distance: nonbonded pdb=" OD1 ASP D 533 " pdb="MG MG D 703 " model vdw 1.971 2.170 nonbonded pdb=" OD1 ASP F 533 " pdb="MG MG F 703 " model vdw 2.028 2.170 nonbonded pdb=" NE2 HIS D 448 " pdb="MG MG D 703 " model vdw 2.042 2.250 nonbonded pdb=" NE2 HIS C 245 " pdb="MG MG C 703 " model vdw 2.056 2.250 nonbonded pdb=" NE2 HIS A 243 " pdb="MG MG A 703 " model vdw 2.080 2.250 ... (remaining 238524 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 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 703)) selection = (chain 'B' and (resid 2 through 192 or resid 200 through 600 or (resid 701 and ( \ name C2 or name C4 or name C5 or name C6 or name C8 or name N1 or name N3 or nam \ e N6 or name N7 or name N9 )) or (resid 702 and (name O1A or name O1B or name O1 \ G or name O2A or name O2B or name O2G or name O3A or name O3B or name O3G or nam \ e O5' or name PA or name PB or name PG )) or resid 703)) selection = (chain 'C' and (resid 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 703)) selection = (chain 'D' and (resid 2 through 192 or resid 200 through 600 or (resid 701 and ( \ name C2 or name C4 or name C5 or name C6 or name C8 or name N1 or name N3 or nam \ e N6 or name N7 or name N9 )) or (resid 702 and (name O1A or name O1B or name O1 \ G or name O2A or name O2B or name O2G or name O3A or name O3B or name O3G or nam \ e O5' or name PA or name PB or name PG )) or resid 703)) selection = (chain 'E' and (resid 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 701 or (resid 702 and \ (name O1A or name O1B or name O1G or name O2A or name O2B or name O2G or name O \ 3A or name O3B or name O3G or name O5' or name PA or name PB or name PG )) or re \ sid 703)) selection = (chain 'F' and (resid 2 through 192 or resid 200 through 600 or (resid 701 and ( \ name C2 or name C4 or name C5 or name C6 or name C8 or name N1 or name N3 or nam \ e N6 or name N7 or name N9 )) or (resid 702 and (name O1A or name O1B or name O1 \ G or name O2A or name O2B or name O2G or name O3A or name O3B or name O3G or nam \ e O5' or name PA or name PB or name PG )) or resid 703)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.56 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 14.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 24.050 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 0.233 29256 Z= 0.565 Angle : 0.750 16.880 39722 Z= 0.495 Chirality : 0.043 0.306 4396 Planarity : 0.009 0.365 5077 Dihedral : 18.809 89.435 10970 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.65 % Favored : 94.18 % Rotamer: Outliers : 0.52 % Allowed : 31.06 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.36 (0.15), residues: 3558 helix: 1.43 (0.13), residues: 1668 sheet: 0.04 (0.27), residues: 429 loop : -1.10 (0.17), residues: 1461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 346 TYR 0.014 0.001 TYR B 77 PHE 0.015 0.001 PHE F 585 TRP 0.023 0.001 TRP C 157 HIS 0.006 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.57 (29256) covalent geometry : angle 0.74996 / 0.50 (39722) hydrogen bonds : bond 0.15609 / 10.78 ( 1284) hydrogen bonds : angle 6.14267 / 4.42 ( 3696) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 294 MET cc_start: 0.7779 (mmt) cc_final: 0.7521 (mmm) REVERT: D 291 ASP cc_start: 0.9476 (m-30) cc_final: 0.9130 (p0) REVERT: E 151 MET cc_start: 0.5521 (mtt) cc_final: 0.5122 (ppp) REVERT: E 267 ASP cc_start: 0.8778 (p0) cc_final: 0.8533 (p0) REVERT: E 404 MET cc_start: 0.8468 (ttp) cc_final: 0.7607 (tmm) REVERT: E 509 MET cc_start: 0.7299 (ptm) cc_final: 0.7089 (ptm) outliers start: 16 outliers final: 7 residues processed: 144 average time/residue: 0.1868 time to fit residues: 44.5950 Evaluate side-chains 114 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain D residue 430 TYR Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 99 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 HIS ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN A 356 ASN A 406 GLN A 475 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 111 GLN C 353 GLN C 406 GLN ** C 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 ASN E 258 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 406 GLN F 460 GLN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.040199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.027592 restraints weight = 251160.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.028569 restraints weight = 159131.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.029185 restraints weight = 122000.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.029571 restraints weight = 104357.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.029710 restraints weight = 95017.585| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2935 r_free = 0.2935 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29256 Z= 0.168 Angle : 0.597 10.675 39722 Z= 0.306 Chirality : 0.041 0.193 4396 Planarity : 0.004 0.061 5077 Dihedral : 10.352 89.947 4191 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 2.44 % Allowed : 29.37 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.56 (0.15), residues: 3558 helix: 1.61 (0.13), residues: 1719 sheet: 0.07 (0.26), residues: 432 loop : -1.09 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 558 TYR 0.015 0.001 TYR C 591 PHE 0.020 0.001 PHE F 585 TRP 0.009 0.001 TRP F 349 HIS 0.007 0.001 HIS E 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (29256) covalent geometry : angle 0.59650 / 0.31 (39722) hydrogen bonds : bond 0.04150 / 2.79 ( 1284) hydrogen bonds : angle 4.76458 / 3.41 ( 3696) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 108 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 SER cc_start: 0.9505 (OUTLIER) cc_final: 0.9164 (p) REVERT: A 294 MET cc_start: 0.9094 (mmm) cc_final: 0.8867 (mmm) REVERT: B 89 MET cc_start: 0.8745 (mtp) cc_final: 0.8445 (mpp) REVERT: B 196 MET cc_start: 0.8683 (tpp) cc_final: 0.8480 (tpp) REVERT: B 494 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8405 (pt0) REVERT: B 548 ILE cc_start: 0.9544 (OUTLIER) cc_final: 0.9309 (tp) REVERT: B 580 MET cc_start: 0.8925 (mmm) cc_final: 0.8620 (mtp) REVERT: D 483 MET cc_start: 0.9073 (mtp) cc_final: 0.8800 (mtm) REVERT: E 151 MET cc_start: 0.6755 (mtt) cc_final: 0.5514 (ppp) REVERT: E 257 ASP cc_start: 0.9709 (OUTLIER) cc_final: 0.9406 (p0) REVERT: E 404 MET cc_start: 0.9287 (ttp) cc_final: 0.8464 (tmm) REVERT: F 208 PHE cc_start: 0.7630 (m-80) cc_final: 0.7125 (m-80) REVERT: F 483 MET cc_start: 0.9352 (ttm) cc_final: 0.9087 (ttm) REVERT: F 494 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: F 559 MET cc_start: 0.9462 (tpp) cc_final: 0.9175 (tpp) outliers start: 75 outliers final: 23 residues processed: 179 average time/residue: 0.1813 time to fit residues: 54.9153 Evaluate side-chains 133 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 430 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 97 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 234 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 320 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 186 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 472 HIS ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 ASN ** F 502 GLN ** 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 = 0.3370 r_free = 0.3370 target = 0.039418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.026778 restraints weight = 249193.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.027720 restraints weight = 158256.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.028319 restraints weight = 122251.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.028694 restraints weight = 104815.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028923 restraints weight = 95524.067| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29256 Z= 0.199 Angle : 0.609 11.421 39722 Z= 0.312 Chirality : 0.042 0.294 4396 Planarity : 0.004 0.045 5077 Dihedral : 9.690 88.842 4178 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.45 % Favored : 94.41 % Rotamer: Outliers : 3.18 % Allowed : 28.53 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.61 (0.15), residues: 3558 helix: 1.71 (0.13), residues: 1719 sheet: -0.04 (0.25), residues: 462 loop : -1.12 (0.17), residues: 1377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 566 TYR 0.021 0.001 TYR B 153 PHE 0.021 0.001 PHE B 208 TRP 0.019 0.001 TRP C 157 HIS 0.009 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (29256) covalent geometry : angle 0.60933 / 0.31 (39722) hydrogen bonds : bond 0.03693 / 2.45 ( 1284) hydrogen bonds : angle 4.52617 / 3.25 ( 3696) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 106 time to evaluate : 1.169 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: A 80 MET cc_start: 0.8861 (ttt) cc_final: 0.8609 (ttm) REVERT: A 89 MET cc_start: 0.8639 (mmm) cc_final: 0.8338 (mmm) REVERT: A 107 SER cc_start: 0.9552 (OUTLIER) cc_final: 0.9201 (p) REVERT: A 291 ASP cc_start: 0.9749 (t0) cc_final: 0.9454 (p0) REVERT: A 294 MET cc_start: 0.9113 (mmm) cc_final: 0.8905 (mmm) REVERT: B 89 MET cc_start: 0.8833 (mtp) cc_final: 0.8493 (mpp) REVERT: B 196 MET cc_start: 0.8933 (tpp) cc_final: 0.8559 (tpp) REVERT: B 483 MET cc_start: 0.9379 (mtp) cc_final: 0.9138 (mtm) REVERT: B 494 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: B 548 ILE cc_start: 0.9598 (OUTLIER) cc_final: 0.9373 (tp) REVERT: C 80 MET cc_start: 0.8941 (mtm) cc_final: 0.8480 (mtm) REVERT: D 167 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8697 (mm) REVERT: D 291 ASP cc_start: 0.9847 (m-30) cc_final: 0.9552 (p0) REVERT: D 483 MET cc_start: 0.9149 (mtp) cc_final: 0.8844 (mtm) REVERT: D 559 MET cc_start: 0.9312 (tpp) cc_final: 0.9084 (tpp) REVERT: E 151 MET cc_start: 0.7649 (mtt) cc_final: 0.7279 (ppp) REVERT: E 320 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.9122 (tp-100) REVERT: E 404 MET cc_start: 0.9287 (ttp) cc_final: 0.8507 (tmm) REVERT: F 89 MET cc_start: 0.9170 (mmm) cc_final: 0.8718 (tpp) REVERT: F 208 PHE cc_start: 0.7716 (m-80) cc_final: 0.7270 (m-80) REVERT: F 483 MET cc_start: 0.9417 (ttm) cc_final: 0.9058 (ttm) REVERT: F 559 MET cc_start: 0.9446 (tpp) cc_final: 0.9148 (tpp) outliers start: 98 outliers final: 40 residues processed: 196 average time/residue: 0.1597 time to fit residues: 53.5632 Evaluate side-chains 145 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 100 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 107 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 320 GLN Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain E residue 557 SER Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 282 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 176 optimal weight: 1.9990 chunk 252 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 278 optimal weight: 2.9990 chunk 291 optimal weight: 0.9980 chunk 194 optimal weight: 0.1980 chunk 286 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 166 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN E 145 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS E 343 ASN ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 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 = 0.3382 r_free = 0.3382 target = 0.039800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.027191 restraints weight = 245816.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.028142 restraints weight = 156188.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028759 restraints weight = 120324.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.029146 restraints weight = 102767.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.029356 restraints weight = 93433.600| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29256 Z= 0.113 Angle : 0.552 10.262 39722 Z= 0.280 Chirality : 0.041 0.201 4396 Planarity : 0.003 0.046 5077 Dihedral : 9.539 89.253 4178 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 3.25 % Allowed : 28.30 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.65 (0.15), residues: 3558 helix: 1.73 (0.13), residues: 1719 sheet: 0.04 (0.25), residues: 453 loop : -1.12 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 72 TYR 0.022 0.001 TYR B 153 PHE 0.020 0.001 PHE B 208 TRP 0.012 0.001 TRP C 157 HIS 0.006 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (29256) covalent geometry : angle 0.55205 / 0.28 (39722) hydrogen bonds : bond 0.03363 / 2.24 ( 1284) hydrogen bonds : angle 4.35170 / 3.11 ( 3696) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 103 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8853 (ttt) cc_final: 0.8584 (ttm) REVERT: A 89 MET cc_start: 0.8698 (mmm) cc_final: 0.8347 (mmm) REVERT: A 291 ASP cc_start: 0.9749 (t0) cc_final: 0.9464 (p0) REVERT: A 294 MET cc_start: 0.9151 (mmm) cc_final: 0.8927 (mmm) REVERT: A 404 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8860 (ttm) REVERT: A 483 MET cc_start: 0.9226 (mtt) cc_final: 0.8968 (mtt) REVERT: B 14 MET cc_start: 0.8058 (mpp) cc_final: 0.7830 (tpt) REVERT: B 89 MET cc_start: 0.8827 (mtp) cc_final: 0.8518 (mpp) REVERT: B 483 MET cc_start: 0.9383 (mtp) cc_final: 0.9120 (mtm) REVERT: B 494 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: B 548 ILE cc_start: 0.9575 (OUTLIER) cc_final: 0.9345 (tp) REVERT: C 29 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.9000 (pm20) REVERT: C 62 CYS cc_start: 0.7248 (OUTLIER) cc_final: 0.6836 (p) REVERT: C 94 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9152 (mm) REVERT: C 291 ASP cc_start: 0.9569 (m-30) cc_final: 0.9308 (p0) REVERT: D 291 ASP cc_start: 0.9848 (m-30) cc_final: 0.9585 (p0) REVERT: E 151 MET cc_start: 0.7556 (mtt) cc_final: 0.7186 (ppp) REVERT: E 404 MET cc_start: 0.9276 (ttp) cc_final: 0.8534 (tmm) REVERT: E 559 MET cc_start: 0.9212 (tpp) cc_final: 0.8815 (tpp) REVERT: F 208 PHE cc_start: 0.7728 (m-80) cc_final: 0.7249 (m-80) REVERT: F 483 MET cc_start: 0.9458 (ttm) cc_final: 0.9105 (ttm) REVERT: F 559 MET cc_start: 0.9433 (tpp) cc_final: 0.9106 (tpp) outliers start: 100 outliers final: 47 residues processed: 192 average time/residue: 0.1734 time to fit residues: 56.5215 Evaluate side-chains 155 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 102 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 62 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 580 MET Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 543 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 231 optimal weight: 7.9990 chunk 295 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.0980 chunk 242 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 500 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.040116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.027050 restraints weight = 244803.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.027996 restraints weight = 158107.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028609 restraints weight = 122728.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.028991 restraints weight = 105612.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.029230 restraints weight = 96460.261| |-----------------------------------------------------------------------------| r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2910 r_free = 0.2910 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29256 Z= 0.115 Angle : 0.567 11.258 39722 Z= 0.284 Chirality : 0.041 0.217 4396 Planarity : 0.003 0.039 5077 Dihedral : 9.348 89.863 4177 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 2.70 % Allowed : 28.46 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.67 (0.15), residues: 3558 helix: 1.74 (0.13), residues: 1719 sheet: 0.10 (0.25), residues: 453 loop : -1.12 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.017 0.001 TYR B 153 PHE 0.021 0.001 PHE B 208 TRP 0.013 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (29256) covalent geometry : angle 0.56727 / 0.28 (39722) hydrogen bonds : bond 0.03261 / 2.18 ( 1284) hydrogen bonds : angle 4.28908 / 3.07 ( 3696) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 102 time to evaluate : 1.153 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: A 80 MET cc_start: 0.8837 (ttt) cc_final: 0.8561 (ttm) REVERT: A 89 MET cc_start: 0.8715 (mmm) cc_final: 0.8332 (mmm) REVERT: A 291 ASP cc_start: 0.9746 (t0) cc_final: 0.9464 (p0) REVERT: A 294 MET cc_start: 0.9147 (mmm) cc_final: 0.8908 (mmm) REVERT: A 404 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8835 (ttm) REVERT: A 483 MET cc_start: 0.9171 (mtt) cc_final: 0.8970 (mtt) REVERT: B 89 MET cc_start: 0.8829 (mtp) cc_final: 0.8520 (mpp) REVERT: B 196 MET cc_start: 0.9017 (tpp) cc_final: 0.8421 (tpp) REVERT: B 483 MET cc_start: 0.9386 (mtp) cc_final: 0.9112 (mtm) REVERT: B 494 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8426 (pt0) REVERT: B 548 ILE cc_start: 0.9587 (OUTLIER) cc_final: 0.9357 (tp) REVERT: C 29 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8855 (mp0) REVERT: C 62 CYS cc_start: 0.7303 (OUTLIER) cc_final: 0.6968 (p) REVERT: C 94 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9170 (mm) REVERT: C 106 MET cc_start: 0.8970 (pmm) cc_final: 0.8620 (pmm) REVERT: C 291 ASP cc_start: 0.9580 (m-30) cc_final: 0.9315 (p0) REVERT: C 559 MET cc_start: 0.9626 (mmm) cc_final: 0.9324 (tpp) REVERT: D 1 MET cc_start: 0.8169 (tmm) cc_final: 0.7772 (tmm) REVERT: D 291 ASP cc_start: 0.9847 (m-30) cc_final: 0.9564 (p0) REVERT: E 151 MET cc_start: 0.7598 (mtt) cc_final: 0.7235 (ppp) REVERT: E 359 PHE cc_start: 0.9619 (OUTLIER) cc_final: 0.9392 (m-10) REVERT: E 404 MET cc_start: 0.9257 (ttp) cc_final: 0.8518 (tmm) REVERT: E 559 MET cc_start: 0.9199 (tpp) cc_final: 0.8914 (tpp) REVERT: F 151 MET cc_start: 0.8416 (ppp) cc_final: 0.8076 (ppp) REVERT: F 208 PHE cc_start: 0.7730 (m-80) cc_final: 0.7276 (m-80) REVERT: F 242 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9360 (mm) REVERT: F 404 MET cc_start: 0.9026 (ttm) cc_final: 0.8737 (mtt) REVERT: F 421 PHE cc_start: 0.6691 (OUTLIER) cc_final: 0.6133 (p90) REVERT: F 483 MET cc_start: 0.9470 (ttm) cc_final: 0.9105 (ttm) REVERT: F 559 MET cc_start: 0.9423 (tpp) cc_final: 0.9096 (tpp) outliers start: 83 outliers final: 57 residues processed: 176 average time/residue: 0.1674 time to fit residues: 50.6583 Evaluate side-chains 167 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 62 CYS Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 580 MET Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 421 PHE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 532 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 181 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 281 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 271 optimal weight: 0.0020 chunk 186 optimal weight: 0.7980 chunk 261 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 213 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN C 46 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS C 475 ASN ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 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 = 0.3394 r_free = 0.3394 target = 0.040105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.027067 restraints weight = 243599.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.028012 restraints weight = 157299.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.028619 restraints weight = 122286.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.028999 restraints weight = 105195.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.029245 restraints weight = 96060.400| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2918 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2918 r_free = 0.2918 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2918 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 29256 Z= 0.105 Angle : 0.558 10.194 39722 Z= 0.278 Chirality : 0.041 0.184 4396 Planarity : 0.003 0.038 5077 Dihedral : 9.140 89.467 4177 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.31 % Favored : 94.58 % Rotamer: Outliers : 2.60 % Allowed : 28.20 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.71 (0.15), residues: 3558 helix: 1.75 (0.13), residues: 1719 sheet: 0.16 (0.26), residues: 453 loop : -1.08 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 3 TYR 0.015 0.001 TYR B 153 PHE 0.023 0.001 PHE D 208 TRP 0.012 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (29256) covalent geometry : angle 0.55775 / 0.28 (39722) hydrogen bonds : bond 0.03097 / 2.07 ( 1284) hydrogen bonds : angle 4.18326 / 2.99 ( 3696) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 101 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.8976 (pmm) cc_final: 0.8703 (pmm) REVERT: A 80 MET cc_start: 0.8826 (ttt) cc_final: 0.8547 (ttm) REVERT: A 291 ASP cc_start: 0.9744 (t0) cc_final: 0.9468 (p0) REVERT: A 294 MET cc_start: 0.9159 (mmm) cc_final: 0.8907 (mmm) REVERT: B 89 MET cc_start: 0.8840 (mtp) cc_final: 0.8545 (mpp) REVERT: B 483 MET cc_start: 0.9401 (mtp) cc_final: 0.9117 (mtm) REVERT: B 494 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8439 (pt0) REVERT: B 548 ILE cc_start: 0.9576 (OUTLIER) cc_final: 0.9338 (tp) REVERT: C 27 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: C 29 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8876 (mp0) REVERT: C 80 MET cc_start: 0.8798 (mtm) cc_final: 0.8596 (mtm) REVERT: C 94 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9181 (mm) REVERT: C 149 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8714 (mm) REVERT: C 291 ASP cc_start: 0.9579 (m-30) cc_final: 0.9322 (p0) REVERT: D 3 ARG cc_start: 0.9256 (OUTLIER) cc_final: 0.8770 (mtm110) REVERT: D 291 ASP cc_start: 0.9848 (m-30) cc_final: 0.9561 (p0) REVERT: E 151 MET cc_start: 0.7580 (mtt) cc_final: 0.7221 (ppp) REVERT: E 359 PHE cc_start: 0.9620 (OUTLIER) cc_final: 0.9385 (m-10) REVERT: E 404 MET cc_start: 0.9243 (ttp) cc_final: 0.8517 (tmm) REVERT: E 559 MET cc_start: 0.9192 (tpp) cc_final: 0.8894 (tpp) REVERT: F 137 MET cc_start: 0.9119 (pmm) cc_final: 0.8915 (pmm) REVERT: F 151 MET cc_start: 0.8462 (ppp) cc_final: 0.8063 (ppp) REVERT: F 208 PHE cc_start: 0.7724 (m-80) cc_final: 0.7286 (m-80) REVERT: F 242 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9370 (mm) REVERT: F 483 MET cc_start: 0.9480 (ttm) cc_final: 0.9185 (ttm) REVERT: F 559 MET cc_start: 0.9419 (tpp) cc_final: 0.9094 (tpp) outliers start: 80 outliers final: 56 residues processed: 172 average time/residue: 0.1690 time to fit residues: 49.9289 Evaluate side-chains 165 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 100 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 580 MET Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 134 optimal weight: 0.0010 chunk 17 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 157 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.039440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.026968 restraints weight = 247079.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.027904 restraints weight = 156317.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.028491 restraints weight = 120398.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.028859 restraints weight = 103233.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.029088 restraints weight = 94181.507| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29256 Z= 0.140 Angle : 0.572 13.388 39722 Z= 0.285 Chirality : 0.041 0.185 4396 Planarity : 0.003 0.038 5077 Dihedral : 8.980 88.699 4177 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 2.53 % Allowed : 28.56 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % 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 are not related in a simple way. whole: 0.80 (0.15), residues: 3558 helix: 1.87 (0.13), residues: 1701 sheet: 0.16 (0.26), residues: 453 loop : -1.05 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 3 TYR 0.014 0.001 TYR B 153 PHE 0.022 0.001 PHE D 208 TRP 0.012 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (29256) covalent geometry : angle 0.57211 / 0.29 (39722) hydrogen bonds : bond 0.03108 / 2.07 ( 1284) hydrogen bonds : angle 4.19103 / 3.00 ( 3696) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7116 Ramachandran restraints generated. 3558 Oldfield, 0 Emsley, 3558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 100 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8856 (ttt) cc_final: 0.8639 (ttm) REVERT: A 89 MET cc_start: 0.8883 (tpp) cc_final: 0.8128 (mmm) REVERT: A 291 ASP cc_start: 0.9740 (t0) cc_final: 0.9467 (p0) REVERT: A 294 MET cc_start: 0.9178 (mmm) cc_final: 0.8933 (mmm) REVERT: B 89 MET cc_start: 0.8891 (mtp) cc_final: 0.8630 (mpp) REVERT: B 196 MET cc_start: 0.8985 (tpp) cc_final: 0.8297 (tpp) REVERT: B 494 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8521 (pt0) REVERT: B 548 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9343 (tp) REVERT: C 27 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8148 (m-80) REVERT: C 94 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9197 (mm) REVERT: C 106 MET cc_start: 0.8994 (pmm) cc_final: 0.8570 (pmm) REVERT: C 291 ASP cc_start: 0.9560 (m-30) cc_final: 0.9322 (p0) REVERT: D 1 MET cc_start: 0.8121 (tmm) cc_final: 0.7597 (tmm) REVERT: D 3 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8744 (mtm110) REVERT: E 359 PHE cc_start: 0.9647 (OUTLIER) cc_final: 0.9418 (m-10) REVERT: E 404 MET cc_start: 0.9237 (ttp) cc_final: 0.8511 (tmm) REVERT: E 559 MET cc_start: 0.9258 (tpp) cc_final: 0.8929 (tpp) REVERT: F 151 MET cc_start: 0.8673 (ppp) cc_final: 0.8265 (ppp) REVERT: F 208 PHE cc_start: 0.7743 (m-80) cc_final: 0.7301 (m-80) REVERT: F 242 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9406 (mm) REVERT: F 404 MET cc_start: 0.9056 (ttm) cc_final: 0.8676 (mtt) REVERT: F 483 MET cc_start: 0.9492 (ttm) cc_final: 0.9179 (ttm) REVERT: F 559 MET cc_start: 0.9436 (tpp) cc_final: 0.9068 (tpp) outliers start: 78 outliers final: 61 residues processed: 172 average time/residue: 0.1800 time to fit residues: 52.7091 Evaluate side-chains 168 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 100 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 157 TRP Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 186 ILE Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 303 LYS Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 188 GLU Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.1573 > 50: distance: 74 - 95: 11.763 distance: 78 - 106: 5.689 distance: 86 - 115: 3.191 distance: 89 - 95: 14.467 distance: 90 - 123: 14.752 distance: 95 - 96: 14.194 distance: 96 - 97: 8.463 distance: 96 - 99: 10.139 distance: 97 - 98: 18.226 distance: 97 - 106: 16.849 distance: 98 - 135: 19.225 distance: 99 - 100: 6.198 distance: 100 - 101: 13.762 distance: 101 - 102: 6.233 distance: 102 - 103: 10.328 distance: 103 - 104: 10.932 distance: 103 - 105: 6.278 distance: 107 - 108: 8.048 distance: 107 - 110: 9.010 distance: 108 - 109: 8.023 distance: 108 - 115: 3.607 distance: 109 - 143: 17.351 distance: 110 - 111: 16.877 distance: 111 - 112: 18.289 distance: 112 - 113: 7.392 distance: 113 - 114: 11.117 distance: 115 - 116: 3.473 distance: 116 - 117: 11.126 distance: 116 - 119: 9.426 distance: 117 - 118: 4.290 distance: 117 - 123: 3.127 distance: 118 - 150: 28.853 distance: 119 - 120: 5.965 distance: 119 - 121: 15.313 distance: 120 - 122: 15.668 distance: 123 - 124: 14.249 distance: 124 - 125: 14.375 distance: 124 - 127: 14.388 distance: 125 - 126: 12.214 distance: 125 - 135: 13.434 distance: 126 - 156: 16.056 distance: 127 - 128: 8.137 distance: 128 - 129: 9.029 distance: 128 - 130: 3.352 distance: 129 - 131: 5.661 distance: 130 - 132: 8.850 distance: 131 - 133: 3.890 distance: 132 - 133: 5.939 distance: 133 - 134: 15.535 distance: 135 - 136: 4.040 distance: 136 - 137: 11.322 distance: 136 - 139: 13.885 distance: 137 - 138: 12.713 distance: 137 - 143: 10.620 distance: 138 - 164: 15.564 distance: 139 - 140: 13.120 distance: 140 - 141: 18.211 distance: 140 - 142: 17.497 distance: 143 - 144: 13.825 distance: 144 - 145: 8.525 distance: 144 - 147: 9.636 distance: 145 - 146: 7.746 distance: 145 - 150: 10.152 distance: 147 - 148: 8.748 distance: 147 - 149: 14.935 distance: 150 - 151: 9.945 distance: 151 - 152: 26.328 distance: 151 - 154: 11.933 distance: 152 - 153: 13.721 distance: 152 - 156: 31.652 distance: 154 - 155: 37.015 distance: 156 - 157: 17.815 distance: 157 - 158: 18.239 distance: 157 - 160: 23.784 distance: 158 - 159: 25.855 distance: 158 - 164: 32.548 distance: 160 - 161: 13.497 distance: 161 - 162: 43.641 distance: 161 - 163: 15.603 distance: 164 - 165: 11.577 distance: 165 - 166: 13.580 distance: 165 - 168: 9.748 distance: 166 - 167: 21.628 distance: 166 - 172: 13.831 distance: 168 - 169: 29.193 distance: 168 - 170: 24.060 distance: 169 - 171: 23.796 distance: 172 - 173: 21.956 distance: 173 - 174: 7.914 distance: 173 - 176: 14.328 distance: 174 - 175: 17.220 distance: 174 - 178: 16.455 distance: 176 - 177: 12.703