Starting phenix.real_space_refine on Sat Aug 8 13:48:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdb_45466/08_2026/9cdb_45466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdb_45466/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9cdb_45466/08_2026/9cdb_45466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdb_45466/08_2026/9cdb_45466.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdb_45466/08_2026/9cdb_45466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdb_45466/08_2026/9cdb_45466.cif" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 7.23, per 1000 atoms: 0.25 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.04 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: 6.13 Time building geometry restraints manager: 3.43 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: 3805 0.061 - 0.122: 554 0.122 - 0.184: 26 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: 15.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.590 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.080 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.620 ------------------------------------------------------------------------------- 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 : 0.752 16.880 39722 Z= 0.497 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 0.75189 / 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 : 1.116 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: 0.1838 time to fit residues: 44.0925 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 : 1.120 ------------------------------------------------------------------------------- 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 ** 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 ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 377 ASN F 406 GLN F 460 GLN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.040187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.027568 restraints weight = 251690.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.028549 restraints weight = 158952.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.029168 restraints weight = 121818.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.029552 restraints weight = 104134.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.029788 restraints weight = 94836.833| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 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 = 0.2938 r_free = 0.2938 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: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 29256 Z= 0.171 Angle : 0.597 10.641 39722 Z= 0.307 Chirality : 0.041 0.193 4396 Planarity : 0.004 0.060 5077 Dihedral : 10.301 89.988 4191 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.26 % Favored : 94.60 % Rotamer: Outliers : 2.47 % Allowed : 29.30 % Favored : 68.23 % 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: 0.55 (0.15), residues: 3558 helix: 1.59 (0.13), residues: 1722 sheet: 0.22 (0.27), residues: 417 loop : -1.14 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 3 TYR 0.016 0.001 TYR C 591 PHE 0.021 0.001 PHE F 585 TRP 0.009 0.001 TRP F 349 HIS 0.006 0.001 HIS E 396 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (29256) covalent geometry : angle 0.59739 / 0.31 (39722) hydrogen bonds : bond 0.03884 / 2.60 ( 1284) hydrogen bonds : angle 4.72398 / 3.38 ( 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 184 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 108 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8635 (mmm) cc_final: 0.8384 (mmm) REVERT: A 107 SER cc_start: 0.9507 (OUTLIER) cc_final: 0.9161 (p) REVERT: A 294 MET cc_start: 0.9094 (mmm) cc_final: 0.8784 (mpp) REVERT: B 89 MET cc_start: 0.8767 (mtp) cc_final: 0.8447 (mpp) REVERT: B 494 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8456 (pt0) REVERT: B 548 ILE cc_start: 0.9545 (OUTLIER) cc_final: 0.9314 (tp) REVERT: B 580 MET cc_start: 0.8896 (mmm) cc_final: 0.8574 (mtp) REVERT: C 80 MET cc_start: 0.8883 (mtm) cc_final: 0.8532 (mtm) REVERT: D 483 MET cc_start: 0.9081 (mtp) cc_final: 0.8807 (mtm) REVERT: E 151 MET cc_start: 0.6804 (mtt) cc_final: 0.5555 (ppp) REVERT: E 257 ASP cc_start: 0.9705 (OUTLIER) cc_final: 0.9402 (p0) REVERT: E 404 MET cc_start: 0.9288 (ttp) cc_final: 0.8471 (tmm) REVERT: F 208 PHE cc_start: 0.7671 (m-80) cc_final: 0.7171 (m-80) REVERT: F 483 MET cc_start: 0.9317 (ttm) cc_final: 0.9081 (ttm) REVERT: F 494 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: F 559 MET cc_start: 0.9462 (tpp) cc_final: 0.9179 (tpp) outliers start: 76 outliers final: 25 residues processed: 180 average time/residue: 0.1738 time to fit residues: 53.6315 Evaluate side-chains 135 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 105 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 224 LEU 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 531 ASN 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: 1.9990 chunk 50 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 320 optimal weight: 0.7980 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 25 optimal weight: 0.0070 chunk 186 optimal weight: 0.9980 overall best weight: 1.1602 ------------------------------------------------------------------------------- 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** C 46 ASN ** 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** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3399 r_free = 0.3399 target = 0.040327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.027586 restraints weight = 252328.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.028570 restraints weight = 159283.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.029199 restraints weight = 122225.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.029587 restraints weight = 104539.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.029827 restraints weight = 95228.133| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 29256 Z= 0.124 Angle : 0.562 11.083 39722 Z= 0.286 Chirality : 0.041 0.183 4396 Planarity : 0.003 0.047 5077 Dihedral : 9.815 87.083 4178 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.97 % Favored : 94.88 % Rotamer: Outliers : 2.53 % Allowed : 28.59 % Favored : 68.88 % 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: 0.64 (0.15), residues: 3558 helix: 1.70 (0.13), residues: 1722 sheet: 0.12 (0.26), residues: 432 loop : -1.10 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.019 0.001 TYR B 153 PHE 0.014 0.001 PHE D 585 TRP 0.016 0.001 TRP C 157 HIS 0.009 0.001 HIS E 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (29256) covalent geometry : angle 0.56188 / 0.29 (39722) hydrogen bonds : bond 0.03599 / 2.42 ( 1284) hydrogen bonds : angle 4.46116 / 3.19 ( 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 186 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 108 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8863 (ttt) cc_final: 0.8577 (ttm) REVERT: A 89 MET cc_start: 0.8662 (mmm) cc_final: 0.8392 (mmm) REVERT: A 291 ASP cc_start: 0.9754 (t0) cc_final: 0.9460 (p0) REVERT: A 294 MET cc_start: 0.9059 (mmm) cc_final: 0.8858 (mmm) REVERT: B 89 MET cc_start: 0.8744 (mtp) cc_final: 0.8449 (mpp) REVERT: B 151 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7662 (mpp) REVERT: B 483 MET cc_start: 0.9382 (mtp) cc_final: 0.9101 (mtm) REVERT: B 494 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8450 (pt0) REVERT: B 548 ILE cc_start: 0.9565 (OUTLIER) cc_final: 0.9331 (tp) REVERT: B 559 MET cc_start: 0.8994 (mmm) cc_final: 0.8616 (tpp) REVERT: C 80 MET cc_start: 0.8870 (mtm) cc_final: 0.8296 (mtm) REVERT: C 495 MET cc_start: 0.8563 (pmm) cc_final: 0.8176 (pmm) REVERT: D 196 MET cc_start: 0.9016 (tpp) cc_final: 0.8347 (tpp) REVERT: D 208 PHE cc_start: 0.7180 (m-80) cc_final: 0.6966 (m-80) REVERT: D 291 ASP cc_start: 0.9843 (m-30) cc_final: 0.9570 (p0) REVERT: D 483 MET cc_start: 0.9142 (mtp) cc_final: 0.8846 (mtm) REVERT: D 559 MET cc_start: 0.9223 (tpp) cc_final: 0.8891 (tpp) REVERT: E 137 MET cc_start: 0.8575 (pmm) cc_final: 0.8373 (pmm) REVERT: E 151 MET cc_start: 0.6978 (mtt) cc_final: 0.5777 (ppp) REVERT: E 404 MET cc_start: 0.9295 (ttp) cc_final: 0.8463 (tmm) REVERT: F 208 PHE cc_start: 0.7697 (m-80) cc_final: 0.7205 (m-80) REVERT: F 483 MET cc_start: 0.9395 (ttm) cc_final: 0.9071 (ttm) REVERT: F 559 MET cc_start: 0.9457 (tpp) cc_final: 0.9142 (tpp) outliers start: 78 outliers final: 33 residues processed: 178 average time/residue: 0.1749 time to fit residues: 53.4000 Evaluate side-chains 138 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 102 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 448 HIS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 151 MET 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 531 ASN 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 191 SER Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 149 ILE 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 182 ILE Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 549 LEU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 97 VAL 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 494 GLU Chi-restraints excluded: chain F residue 532 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 282 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 176 optimal weight: 0.5980 chunk 252 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 278 optimal weight: 8.9990 chunk 291 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 286 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 166 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.040631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.028557 restraints weight = 242615.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.029506 restraints weight = 152880.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.030117 restraints weight = 117055.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.030500 restraints weight = 99752.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.030732 restraints weight = 90502.959| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 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 = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29256 Z= 0.120 Angle : 0.552 10.289 39722 Z= 0.280 Chirality : 0.041 0.204 4396 Planarity : 0.003 0.040 5077 Dihedral : 9.539 87.504 4177 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 2.79 % Allowed : 28.17 % Favored : 69.04 % 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: 0.66 (0.15), residues: 3558 helix: 1.73 (0.13), residues: 1719 sheet: 0.09 (0.26), residues: 453 loop : -1.11 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.013 0.001 TYR B 153 PHE 0.020 0.001 PHE B 208 TRP 0.011 0.001 TRP C 157 HIS 0.006 0.001 HIS C 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (29256) covalent geometry : angle 0.55204 / 0.28 (39722) hydrogen bonds : bond 0.03313 / 2.21 ( 1284) hydrogen bonds : angle 4.34841 / 3.10 ( 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 189 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 103 time to evaluate : 1.101 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: 0.8841 (ttt) cc_final: 0.8538 (ttm) REVERT: A 89 MET cc_start: 0.8692 (mmm) cc_final: 0.8361 (mmm) REVERT: A 291 ASP cc_start: 0.9744 (t0) cc_final: 0.9446 (p0) REVERT: A 294 MET cc_start: 0.9126 (mmm) cc_final: 0.8895 (mmm) REVERT: A 404 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8924 (ttm) REVERT: B 14 MET cc_start: 0.8205 (mpp) cc_final: 0.7932 (tpt) REVERT: B 89 MET cc_start: 0.8812 (mtp) cc_final: 0.8523 (mpp) REVERT: B 151 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7787 (mpp) REVERT: B 483 MET cc_start: 0.9387 (mtp) cc_final: 0.9108 (mtm) REVERT: B 548 ILE cc_start: 0.9559 (OUTLIER) cc_final: 0.9330 (tp) REVERT: C 29 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8971 (pm20) REVERT: C 62 CYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6825 (p) REVERT: C 80 MET cc_start: 0.8827 (mtm) cc_final: 0.8578 (mtm) REVERT: C 94 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9113 (mm) REVERT: C 106 MET cc_start: 0.8952 (pmm) cc_final: 0.8524 (pmm) REVERT: C 495 MET cc_start: 0.8630 (pmm) cc_final: 0.8170 (pmm) REVERT: C 559 MET cc_start: 0.9633 (mmm) cc_final: 0.9330 (tpp) REVERT: D 291 ASP cc_start: 0.9847 (m-30) cc_final: 0.9564 (p0) REVERT: D 483 MET cc_start: 0.9158 (mtp) cc_final: 0.8854 (mtm) REVERT: E 137 MET cc_start: 0.8587 (pmm) cc_final: 0.8175 (pmm) REVERT: E 151 MET cc_start: 0.7119 (mtt) cc_final: 0.5955 (ppp) REVERT: E 404 MET cc_start: 0.9290 (ttp) cc_final: 0.8490 (tmm) REVERT: F 208 PHE cc_start: 0.7722 (m-80) cc_final: 0.7215 (m-80) REVERT: F 483 MET cc_start: 0.9411 (ttm) cc_final: 0.9078 (ttm) REVERT: F 559 MET cc_start: 0.9466 (tpp) cc_final: 0.9142 (tpp) outliers start: 86 outliers final: 45 residues processed: 181 average time/residue: 0.1466 time to fit residues: 45.4951 Evaluate side-chains 153 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 1.120 ------------------------------------------------------------------------------- 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 389 ASP 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 151 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE 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 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 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 125 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 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 183 SER Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 29 GLU Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 97 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 543 SER Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 149 optimal weight: 4.9990 chunk 222 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 chunk 295 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 475 ASN ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.039617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.027496 restraints weight = 243323.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.028460 restraints weight = 153373.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.029079 restraints weight = 118093.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.029463 restraints weight = 100935.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.029697 restraints weight = 91900.981| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 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 = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29256 Z= 0.110 Angle : 0.555 10.370 39722 Z= 0.277 Chirality : 0.041 0.257 4396 Planarity : 0.003 0.039 5077 Dihedral : 9.314 88.808 4177 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.09 % Favored : 94.77 % Rotamer: Outliers : 2.76 % Allowed : 28.01 % Favored : 69.23 % 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: 0.70 (0.15), residues: 3558 helix: 1.75 (0.13), residues: 1719 sheet: 0.14 (0.25), residues: 453 loop : -1.09 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.012 0.001 TYR B 153 PHE 0.022 0.001 PHE B 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 0.00249 / 0.11 (29256) covalent geometry : angle 0.55487 / 0.28 (39722) hydrogen bonds : bond 0.03174 / 2.12 ( 1284) hydrogen bonds : angle 4.26402 / 3.05 ( 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 186 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 101 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8799 (ttt) cc_final: 0.8527 (ttm) REVERT: A 291 ASP cc_start: 0.9739 (t0) cc_final: 0.9442 (p0) REVERT: A 294 MET cc_start: 0.9149 (mmm) cc_final: 0.8914 (mmm) REVERT: A 404 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8890 (ttm) REVERT: A 483 MET cc_start: 0.9157 (mtt) cc_final: 0.8919 (mtt) REVERT: A 485 THR cc_start: 0.9672 (OUTLIER) cc_final: 0.9323 (t) REVERT: B 89 MET cc_start: 0.8823 (mtp) cc_final: 0.8522 (mpp) REVERT: B 151 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7837 (mpp) REVERT: B 483 MET cc_start: 0.9404 (mtp) cc_final: 0.9113 (mtm) REVERT: B 548 ILE cc_start: 0.9566 (OUTLIER) cc_final: 0.9334 (tp) REVERT: C 29 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.8956 (pm20) REVERT: C 80 MET cc_start: 0.8811 (mtm) cc_final: 0.8414 (mtm) REVERT: C 94 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9125 (mm) REVERT: C 149 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8676 (mm) REVERT: C 495 MET cc_start: 0.8658 (pmm) cc_final: 0.8186 (pmm) REVERT: C 559 MET cc_start: 0.9648 (mmm) cc_final: 0.9265 (tpp) REVERT: D 1 MET cc_start: 0.8083 (tmm) cc_final: 0.7670 (tmm) REVERT: D 291 ASP cc_start: 0.9851 (m-30) cc_final: 0.9566 (p0) REVERT: D 483 MET cc_start: 0.9181 (mtp) cc_final: 0.8874 (mtm) REVERT: E 137 MET cc_start: 0.8679 (pmm) cc_final: 0.8135 (pmm) REVERT: E 151 MET cc_start: 0.7173 (mtt) cc_final: 0.6061 (ppp) REVERT: E 404 MET cc_start: 0.9262 (ttp) cc_final: 0.8474 (tmm) REVERT: E 509 MET cc_start: 0.8184 (ppp) cc_final: 0.7981 (ppp) REVERT: F 208 PHE cc_start: 0.7704 (m-80) cc_final: 0.7213 (m-80) REVERT: F 242 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9329 (mm) REVERT: F 421 PHE cc_start: 0.6641 (OUTLIER) cc_final: 0.6137 (p90) REVERT: F 483 MET cc_start: 0.9442 (ttm) cc_final: 0.9106 (ttm) REVERT: F 559 MET cc_start: 0.9459 (tpp) cc_final: 0.9122 (tpp) outliers start: 85 outliers final: 50 residues processed: 180 average time/residue: 0.1425 time to fit residues: 45.1872 Evaluate side-chains 159 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 100 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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 224 LEU 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 485 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 151 MET Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE 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 29 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 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 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 183 SER Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 252 SER 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 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 476 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 181 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 281 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 271 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 261 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 229 optimal weight: 6.9990 chunk 213 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 ** 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 145 GLN E 343 ASN 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 500 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.039021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.026438 restraints weight = 255124.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.027346 restraints weight = 161755.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.027932 restraints weight = 125293.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.028297 restraints weight = 108043.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.028517 restraints weight = 98822.503| |-----------------------------------------------------------------------------| r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2891 r_free = 0.2891 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: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29256 Z= 0.205 Angle : 0.619 11.389 39722 Z= 0.311 Chirality : 0.041 0.189 4396 Planarity : 0.004 0.044 5077 Dihedral : 9.098 88.474 4177 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 2.66 % Allowed : 28.49 % 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: 0.74 (0.15), residues: 3558 helix: 1.78 (0.13), residues: 1719 sheet: 0.15 (0.25), residues: 465 loop : -1.06 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 3 TYR 0.013 0.001 TYR B 153 PHE 0.028 0.001 PHE B 208 TRP 0.012 0.001 TRP C 157 HIS 0.005 0.001 HIS F 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 (29256) covalent geometry : angle 0.61914 / 0.31 (39722) hydrogen bonds : bond 0.03388 / 2.24 ( 1284) hydrogen bonds : angle 4.35370 / 3.13 ( 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 183 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 101 time to evaluate : 1.261 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: 0.9055 (pmm) cc_final: 0.8776 (pmm) REVERT: A 80 MET cc_start: 0.8875 (ttt) cc_final: 0.8668 (ttm) REVERT: A 89 MET cc_start: 0.8940 (tpp) cc_final: 0.8105 (mmm) REVERT: A 107 SER cc_start: 0.9533 (OUTLIER) cc_final: 0.9222 (p) REVERT: A 291 ASP cc_start: 0.9745 (t0) cc_final: 0.9469 (p0) REVERT: A 294 MET cc_start: 0.9176 (mmm) cc_final: 0.8922 (mmm) REVERT: A 404 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8939 (ttm) REVERT: B 89 MET cc_start: 0.8941 (mtp) cc_final: 0.8625 (mpp) REVERT: B 548 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9361 (tp) REVERT: C 27 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8123 (m-80) REVERT: C 29 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.8887 (mp0) REVERT: C 80 MET cc_start: 0.8886 (mtm) cc_final: 0.8460 (mtm) REVERT: C 94 LEU cc_start: 0.9446 (OUTLIER) cc_final: 0.9190 (mm) REVERT: C 106 MET cc_start: 0.9029 (pmm) cc_final: 0.8633 (pmm) REVERT: C 559 MET cc_start: 0.9657 (mmm) cc_final: 0.9436 (tpp) REVERT: D 3 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8734 (mtm110) REVERT: D 291 ASP cc_start: 0.9850 (m-30) cc_final: 0.9572 (p0) REVERT: D 483 MET cc_start: 0.9201 (mtp) cc_final: 0.8883 (mtm) REVERT: E 137 MET cc_start: 0.8862 (pmm) cc_final: 0.8219 (pmm) REVERT: E 151 MET cc_start: 0.7848 (mtt) cc_final: 0.6764 (ppp) REVERT: E 320 GLN cc_start: 0.9392 (OUTLIER) cc_final: 0.9126 (tp-100) REVERT: E 404 MET cc_start: 0.9253 (ttp) cc_final: 0.8540 (tmm) REVERT: E 509 MET cc_start: 0.8448 (ppp) cc_final: 0.8104 (ppp) REVERT: F 151 MET cc_start: 0.8531 (ppp) cc_final: 0.8167 (ppp) REVERT: F 208 PHE cc_start: 0.7755 (m-80) cc_final: 0.7276 (m-80) REVERT: F 242 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9388 (mm) REVERT: F 483 MET cc_start: 0.9461 (ttm) cc_final: 0.9167 (ttm) REVERT: F 559 MET cc_start: 0.9463 (tpp) cc_final: 0.9071 (tpp) outliers start: 82 outliers final: 53 residues processed: 176 average time/residue: 0.1768 time to fit residues: 53.4157 Evaluate side-chains 163 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 101 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 224 LEU 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 B residue 15 VAL 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 189 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE 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 29 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 191 SER 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 125 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 320 GLN 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 189 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 242 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 532 THR Chi-restraints excluded: chain F residue 543 SER 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: 1.9990 chunk 17 optimal weight: 0.1980 chunk 189 optimal weight: 3.9990 chunk 6 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 111 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN E 531 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.038546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.026454 restraints weight = 245997.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.027389 restraints weight = 155834.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.027983 restraints weight = 120512.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.028352 restraints weight = 103348.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.028578 restraints weight = 94341.384| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29256 Z= 0.161 Angle : 0.582 10.644 39722 Z= 0.293 Chirality : 0.041 0.185 4396 Planarity : 0.003 0.039 5077 Dihedral : 8.987 88.201 4177 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 2.73 % Allowed : 28.46 % Favored : 68.81 % 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: 0.72 (0.15), residues: 3558 helix: 1.84 (0.13), residues: 1707 sheet: 0.02 (0.25), residues: 471 loop : -1.11 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 484 TYR 0.017 0.001 TYR B 153 PHE 0.027 0.001 PHE B 208 TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (29256) covalent geometry : angle 0.58172 / 0.29 (39722) hydrogen bonds : bond 0.03226 / 2.16 ( 1284) hydrogen bonds : angle 4.26747 / 3.06 ( 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 183 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 99 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9066 (pmm) cc_final: 0.8786 (pmm) REVERT: A 80 MET cc_start: 0.8852 (ttt) cc_final: 0.8636 (ttm) REVERT: A 89 MET cc_start: 0.8884 (tpp) cc_final: 0.8203 (mmm) REVERT: A 107 SER cc_start: 0.9554 (OUTLIER) cc_final: 0.9287 (p) REVERT: A 291 ASP cc_start: 0.9743 (t0) cc_final: 0.9473 (p0) REVERT: A 294 MET cc_start: 0.9153 (mmm) cc_final: 0.8903 (mmm) REVERT: A 483 MET cc_start: 0.9193 (mtt) cc_final: 0.8987 (mtt) REVERT: B 89 MET cc_start: 0.8932 (mtp) cc_final: 0.8658 (mpp) REVERT: B 133 ASN cc_start: 0.9624 (OUTLIER) cc_final: 0.9391 (t0) REVERT: B 548 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9341 (tp) REVERT: C 27 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: C 29 GLU cc_start: 0.9242 (OUTLIER) cc_final: 0.8907 (mp0) REVERT: C 80 MET cc_start: 0.8908 (mtm) cc_final: 0.8621 (mtm) REVERT: C 94 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9216 (mm) REVERT: C 559 MET cc_start: 0.9645 (mmm) cc_final: 0.9417 (tpp) REVERT: D 1 MET cc_start: 0.8231 (tmm) cc_final: 0.7648 (tmm) REVERT: D 3 ARG cc_start: 0.9263 (OUTLIER) cc_final: 0.8661 (mtm110) REVERT: D 151 MET cc_start: 0.9259 (ppp) cc_final: 0.8978 (ppp) REVERT: D 483 MET cc_start: 0.9193 (mtp) cc_final: 0.8985 (ttm) REVERT: E 14 MET cc_start: 0.8945 (tpt) cc_final: 0.8448 (tpp) REVERT: E 359 PHE cc_start: 0.9663 (OUTLIER) cc_final: 0.9454 (m-10) REVERT: E 404 MET cc_start: 0.9238 (ttp) cc_final: 0.8612 (tmm) REVERT: E 509 MET cc_start: 0.8437 (ppp) cc_final: 0.8122 (ppp) REVERT: F 151 MET cc_start: 0.8731 (ppp) cc_final: 0.8343 (ppp) REVERT: F 242 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9387 (mm) REVERT: F 404 MET cc_start: 0.9138 (tpp) cc_final: 0.8895 (tpp) REVERT: F 421 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.6199 (p90) REVERT: F 483 MET cc_start: 0.9477 (ttm) cc_final: 0.9193 (ttm) outliers start: 84 outliers final: 50 residues processed: 178 average time/residue: 0.1739 time to fit residues: 53.0904 Evaluate side-chains 159 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 99 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 224 LEU 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 44 VAL Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE 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 29 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 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 252 SER Chi-restraints excluded: chain E residue 359 PHE 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 421 PHE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 62 optimal weight: 7.9990 chunk 296 optimal weight: 0.6980 chunk 6 optimal weight: 20.0000 chunk 272 optimal weight: 0.9990 chunk 213 optimal weight: 0.2980 chunk 216 optimal weight: 9.9990 chunk 150 optimal weight: 0.8980 chunk 28 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 156 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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 ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 145 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.039102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.027100 restraints weight = 246286.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.028019 restraints weight = 158181.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.028598 restraints weight = 122630.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.028962 restraints weight = 105506.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.029178 restraints weight = 96429.289| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 29256 Z= 0.111 Angle : 0.584 15.133 39722 Z= 0.288 Chirality : 0.041 0.227 4396 Planarity : 0.003 0.038 5077 Dihedral : 8.903 88.701 4177 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 2.34 % Allowed : 28.53 % Favored : 69.14 % 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: 0.79 (0.15), residues: 3558 helix: 1.83 (0.13), residues: 1701 sheet: 0.19 (0.26), residues: 453 loop : -1.02 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 427 TYR 0.014 0.001 TYR B 153 PHE 0.027 0.001 PHE F 208 TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (29256) covalent geometry : angle 0.58412 / 0.29 (39722) hydrogen bonds : bond 0.03132 / 2.09 ( 1284) hydrogen bonds : angle 4.18220 / 2.99 ( 3696) *********************** REFINEMENT MACRO_CYCLE 8 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 172 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 100 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9028 (pmm) cc_final: 0.8756 (pmm) REVERT: A 80 MET cc_start: 0.8837 (ttt) cc_final: 0.8621 (ttm) REVERT: A 89 MET cc_start: 0.8967 (tpp) cc_final: 0.8258 (mmm) REVERT: A 107 SER cc_start: 0.9566 (OUTLIER) cc_final: 0.9281 (p) REVERT: A 291 ASP cc_start: 0.9738 (t0) cc_final: 0.9467 (p0) REVERT: A 294 MET cc_start: 0.9156 (mmm) cc_final: 0.8901 (mmm) REVERT: B 89 MET cc_start: 0.8862 (mtp) cc_final: 0.8645 (mpp) REVERT: B 106 MET cc_start: 0.8752 (ptp) cc_final: 0.8397 (ptp) REVERT: B 548 ILE cc_start: 0.9574 (OUTLIER) cc_final: 0.9327 (tp) REVERT: C 27 PHE cc_start: 0.8595 (OUTLIER) cc_final: 0.8152 (m-80) REVERT: C 29 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8919 (mp0) REVERT: C 80 MET cc_start: 0.8867 (mtm) cc_final: 0.8574 (mtm) REVERT: C 94 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9226 (mm) REVERT: C 559 MET cc_start: 0.9641 (mmm) cc_final: 0.9424 (tpp) REVERT: D 1 MET cc_start: 0.8127 (tmm) cc_final: 0.7632 (tmm) REVERT: D 3 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8750 (mtm110) REVERT: D 151 MET cc_start: 0.9235 (ppp) cc_final: 0.8943 (ppp) REVERT: D 483 MET cc_start: 0.9167 (mtp) cc_final: 0.8958 (ttm) REVERT: E 359 PHE cc_start: 0.9663 (OUTLIER) cc_final: 0.9436 (m-10) REVERT: E 404 MET cc_start: 0.9215 (ttp) cc_final: 0.8609 (tmm) REVERT: E 509 MET cc_start: 0.8292 (ppp) cc_final: 0.8024 (ppp) REVERT: F 137 MET cc_start: 0.9191 (pmm) cc_final: 0.8926 (pmm) REVERT: F 151 MET cc_start: 0.8817 (ppp) cc_final: 0.8353 (ppp) REVERT: F 242 LEU cc_start: 0.9638 (OUTLIER) cc_final: 0.9393 (mm) REVERT: F 483 MET cc_start: 0.9490 (ttm) cc_final: 0.9140 (ttm) outliers start: 72 outliers final: 49 residues processed: 168 average time/residue: 0.1694 time to fit residues: 49.5859 Evaluate side-chains 157 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 100 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 107 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 157 TRP Chi-restraints excluded: chain A residue 224 LEU 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 44 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE 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 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 528 VAL Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 44 VAL 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 252 SER Chi-restraints excluded: chain E residue 359 PHE 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 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 543 SER Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 37 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 330 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.038182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.026133 restraints weight = 247513.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.027068 restraints weight = 157280.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.027656 restraints weight = 121539.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.028027 restraints weight = 104231.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.028249 restraints weight = 95022.084| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 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: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 29256 Z= 0.188 Angle : 0.627 14.071 39722 Z= 0.313 Chirality : 0.042 0.260 4396 Planarity : 0.004 0.039 5077 Dihedral : 8.779 87.733 4177 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.68 % Favored : 94.21 % Rotamer: Outliers : 2.47 % Allowed : 28.40 % Favored : 69.14 % 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: 0.79 (0.15), residues: 3558 helix: 1.86 (0.13), residues: 1704 sheet: 0.06 (0.25), residues: 471 loop : -1.03 (0.18), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 132 TYR 0.017 0.001 TYR B 153 PHE 0.027 0.001 PHE B 208 TRP 0.014 0.001 TRP C 157 HIS 0.007 0.001 HIS D 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (29256) covalent geometry : angle 0.62739 / 0.31 (39722) hydrogen bonds : bond 0.03332 / 2.20 ( 1284) hydrogen bonds : angle 4.27238 / 3.07 ( 3696) *********************** REFINEMENT MACRO_CYCLE 9 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 176 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 100 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9072 (pmm) cc_final: 0.8828 (pmm) REVERT: A 80 MET cc_start: 0.8880 (ttt) cc_final: 0.8671 (ttm) REVERT: A 89 MET cc_start: 0.8953 (tpp) cc_final: 0.8234 (mmm) REVERT: A 107 SER cc_start: 0.9559 (OUTLIER) cc_final: 0.9232 (p) REVERT: A 291 ASP cc_start: 0.9740 (t0) cc_final: 0.9473 (p0) REVERT: A 294 MET cc_start: 0.9209 (mmm) cc_final: 0.8955 (mmm) REVERT: B 106 MET cc_start: 0.8799 (ptp) cc_final: 0.8434 (ptp) REVERT: B 548 ILE cc_start: 0.9599 (OUTLIER) cc_final: 0.9366 (tp) REVERT: C 27 PHE cc_start: 0.8510 (OUTLIER) cc_final: 0.8269 (m-80) REVERT: C 80 MET cc_start: 0.8897 (mtm) cc_final: 0.8595 (mtm) REVERT: C 94 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9234 (mm) REVERT: C 106 MET cc_start: 0.8952 (pmm) cc_final: 0.8480 (pmm) REVERT: C 559 MET cc_start: 0.9654 (mmm) cc_final: 0.9380 (tpp) REVERT: D 1 MET cc_start: 0.8165 (tmm) cc_final: 0.7736 (tmm) REVERT: D 3 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8649 (mtm110) REVERT: D 151 MET cc_start: 0.9294 (ppp) cc_final: 0.9004 (ppp) REVERT: D 483 MET cc_start: 0.9189 (mtp) cc_final: 0.8961 (ttm) REVERT: E 14 MET cc_start: 0.8744 (tpt) cc_final: 0.8365 (tpp) REVERT: E 359 PHE cc_start: 0.9686 (OUTLIER) cc_final: 0.9473 (m-10) REVERT: E 404 MET cc_start: 0.9229 (ttp) cc_final: 0.8646 (tmm) REVERT: F 242 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9413 (mm) REVERT: F 421 PHE cc_start: 0.6717 (OUTLIER) cc_final: 0.6217 (p90) REVERT: F 483 MET cc_start: 0.9528 (ttm) cc_final: 0.9224 (ttm) outliers start: 76 outliers final: 55 residues processed: 168 average time/residue: 0.1690 time to fit residues: 49.2722 Evaluate side-chains 163 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 100 time to evaluate : 0.911 ------------------------------------------------------------------------------- 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 310 CYS 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 B residue 44 VAL Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE 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 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 191 SER Chi-restraints excluded: chain C residue 359 PHE 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 252 SER Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 359 PHE 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 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 267 ASP Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 404 MET 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 Chi-restraints excluded: chain F residue 543 SER Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 51 optimal weight: 0.0070 chunk 31 optimal weight: 4.9990 chunk 298 optimal weight: 0.0670 chunk 212 optimal weight: 0.9980 chunk 337 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 243 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 278 optimal weight: 3.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.038907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.026964 restraints weight = 243517.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.027904 restraints weight = 153366.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.028503 restraints weight = 118274.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.028874 restraints weight = 101421.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.029099 restraints weight = 92535.904| |-----------------------------------------------------------------------------| r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 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 = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.029 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 29256 Z= 0.108 Angle : 0.607 14.652 39722 Z= 0.298 Chirality : 0.041 0.189 4396 Planarity : 0.003 0.040 5077 Dihedral : 8.729 89.028 4177 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.42 % Favored : 94.46 % Rotamer: Outliers : 1.98 % Allowed : 28.88 % Favored : 69.14 % 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: 0.77 (0.15), residues: 3558 helix: 1.80 (0.13), residues: 1707 sheet: 0.21 (0.25), residues: 453 loop : -1.01 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.014 0.001 TYR B 153 PHE 0.024 0.001 PHE D 208 TRP 0.014 0.001 TRP C 157 HIS 0.006 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (29256) covalent geometry : angle 0.60705 / 0.30 (39722) hydrogen bonds : bond 0.03128 / 2.09 ( 1284) hydrogen bonds : angle 4.13545 / 2.96 ( 3696) ********************** REFINEMENT MACRO_CYCLE 10 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 163 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 102 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9010 (pmm) cc_final: 0.8741 (pmm) REVERT: A 80 MET cc_start: 0.8845 (ttt) cc_final: 0.8634 (ttm) REVERT: A 89 MET cc_start: 0.8954 (tpp) cc_final: 0.8176 (mmm) REVERT: A 107 SER cc_start: 0.9552 (OUTLIER) cc_final: 0.9253 (p) REVERT: A 291 ASP cc_start: 0.9737 (t0) cc_final: 0.9463 (p0) REVERT: A 294 MET cc_start: 0.9187 (mmm) cc_final: 0.8955 (mmm) REVERT: B 106 MET cc_start: 0.8820 (ptp) cc_final: 0.8464 (ptp) REVERT: B 151 MET cc_start: 0.8844 (ttm) cc_final: 0.8486 (mpp) REVERT: B 384 ARG cc_start: 0.4665 (OUTLIER) cc_final: 0.4048 (mtm180) REVERT: B 548 ILE cc_start: 0.9585 (OUTLIER) cc_final: 0.9344 (tp) REVERT: C 27 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: C 80 MET cc_start: 0.8870 (mtm) cc_final: 0.8562 (mtm) REVERT: C 94 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9214 (mm) REVERT: C 106 MET cc_start: 0.8932 (pmm) cc_final: 0.8451 (pmm) REVERT: C 559 MET cc_start: 0.9626 (mmm) cc_final: 0.9389 (tpp) REVERT: D 1 MET cc_start: 0.8143 (tmm) cc_final: 0.7216 (tmm) REVERT: D 3 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.8535 (mtm110) REVERT: D 151 MET cc_start: 0.9262 (ppp) cc_final: 0.8964 (ppp) REVERT: D 483 MET cc_start: 0.9157 (mtp) cc_final: 0.8937 (ttm) REVERT: D 580 MET cc_start: 0.9105 (mmm) cc_final: 0.8886 (mpp) REVERT: E 14 MET cc_start: 0.8665 (tpt) cc_final: 0.8026 (tpp) REVERT: E 359 PHE cc_start: 0.9675 (OUTLIER) cc_final: 0.9439 (m-10) REVERT: E 404 MET cc_start: 0.9211 (ttp) cc_final: 0.8681 (tmm) REVERT: F 242 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9366 (mm) REVERT: F 483 MET cc_start: 0.9538 (ttm) cc_final: 0.9234 (ttm) outliers start: 61 outliers final: 48 residues processed: 158 average time/residue: 0.1739 time to fit residues: 47.4007 Evaluate side-chains 158 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 102 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 107 SER 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 389 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG 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 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 359 PHE 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 303 LYS Chi-restraints excluded: chain D residue 359 PHE 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 359 PHE 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 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 404 MET 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 Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 221 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 chunk 229 optimal weight: 0.9990 chunk 216 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 136 optimal weight: 0.9980 chunk 271 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 overall best weight: 0.8042 ------------------------------------------------------------------------------- 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** ** 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 = 0.3388 r_free = 0.3388 target = 0.039777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.026808 restraints weight = 244762.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.027756 restraints weight = 158410.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.028357 restraints weight = 123287.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028730 restraints weight = 106233.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028965 restraints weight = 97157.965| |-----------------------------------------------------------------------------| r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2909 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2909 r_free = 0.2909 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: 0.2909 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3080 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= 0.111 Angle : 0.595 14.638 39722 Z= 0.292 Chirality : 0.041 0.207 4396 Planarity : 0.003 0.042 5077 Dihedral : 8.595 89.881 4177 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.40 % Favored : 94.49 % Rotamer: Outliers : 1.98 % Allowed : 28.82 % 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: 0.80 (0.15), residues: 3558 helix: 1.82 (0.13), residues: 1701 sheet: 0.18 (0.25), residues: 459 loop : -0.97 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 3 TYR 0.014 0.001 TYR B 153 PHE 0.022 0.001 PHE B 208 TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (29256) covalent geometry : angle 0.59500 / 0.29 (39722) hydrogen bonds : bond 0.03061 / 2.04 ( 1284) hydrogen bonds : angle 4.10217 / 2.94 ( 3696) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4953.19 seconds wall clock time: 87 minutes 1.44 seconds (5221.44 seconds total)