Starting phenix.real_space_refine on Tue Jun 24 13:54:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cdb_45466/06_2025/9cdb_45466.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cdb_45466/06_2025/9cdb_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_45466/06_2025/9cdb_45466.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cdb_45466/06_2025/9cdb_45466.map" model { file = "/net/cci-nas-00/data/ceres_data/9cdb_45466/06_2025/9cdb_45466.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cdb_45466/06_2025/9cdb_45466.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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:plan2': 1, ' A%rna3p_pur:plan': 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:plan2': 1, ' A%rna3p_pur:plan': 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:plan2': 1, ' A%rna3p_pur:plan': 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: 21.12, per 1000 atoms: 0.74 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: 9.16 Conformation dependent library (CDL) restraints added in 4.1 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: 3.94 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: 11.69 Time building geometry restraints manager: 9.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 9433 1.35 - 1.46: 6581 1.46 - 1.58: 12927 1.58 - 1.70: 69 1.70 - 1.82: 246 Bond restraints: 29256 Sorted by residual: bond pdb=" C1' ATP F 701 " pdb=" C2' ATP F 701 " ideal model delta sigma weight residual 1.531 1.298 0.233 1.20e-02 6.94e+03 3.78e+02 bond pdb=" C1' ATP B 701 " pdb=" C2' ATP B 701 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.69e+02 bond pdb=" C1' ATP F 702 " pdb=" C2' ATP F 702 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.59e+02 bond pdb=" C1' ATP D 701 " pdb=" C2' ATP D 701 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.59e+02 bond pdb=" C1' ATP B 702 " pdb=" C2' ATP B 702 " ideal model delta sigma weight residual 1.531 1.304 0.227 1.20e-02 6.94e+03 3.58e+02 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 39405 3.38 - 6.75: 231 6.75 - 10.13: 66 10.13 - 13.50: 12 13.50 - 16.88: 8 Bond angle restraints: 39722 Sorted by residual: angle pdb=" PB ATP D 702 " pdb=" O3B ATP D 702 " pdb=" PG ATP D 702 " ideal model delta sigma weight residual 139.87 122.99 16.88 1.00e+00 1.00e+00 2.85e+02 angle pdb=" PB ATP D 701 " pdb=" O3B ATP D 701 " pdb=" PG ATP D 701 " ideal model delta sigma weight residual 139.87 123.19 16.68 1.00e+00 1.00e+00 2.78e+02 angle pdb=" PB ATP B 702 " pdb=" O3B ATP B 702 " pdb=" PG ATP B 702 " ideal model delta sigma weight residual 139.87 123.22 16.65 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP F 701 " pdb=" O3B ATP F 701 " pdb=" PG ATP F 701 " ideal model delta sigma weight residual 139.87 123.23 16.64 1.00e+00 1.00e+00 2.77e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 123.41 16.46 1.00e+00 1.00e+00 2.71e+02 ... (remaining 39717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14782 17.89 - 35.77: 2108 35.77 - 53.66: 614 53.66 - 71.55: 136 71.55 - 89.43: 62 Dihedral angle restraints: 17702 sinusoidal: 7301 harmonic: 10401 Sorted by residual: dihedral pdb=" CD ARG F 588 " pdb=" NE ARG F 588 " pdb=" CZ ARG F 588 " pdb=" NH1 ARG F 588 " ideal model delta sinusoidal sigma weight residual 0.00 -48.79 48.79 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA LEU B 211 " pdb=" C LEU B 211 " pdb=" N ALA B 212 " pdb=" CA ALA B 212 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CD ARG B 588 " pdb=" NE ARG B 588 " pdb=" CZ ARG B 588 " pdb=" NH1 ARG B 588 " ideal model delta sinusoidal sigma weight residual 0.00 42.80 -42.80 1 1.00e+01 1.00e-02 2.56e+01 ... (remaining 17699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3814 0.061 - 0.122: 550 0.122 - 0.184: 21 0.184 - 0.245: 3 0.245 - 0.306: 8 Chirality restraints: 4396 Sorted by residual: chirality pdb=" C2' ATP D 701 " pdb=" C1' ATP D 701 " pdb=" C3' ATP D 701 " pdb=" O2' ATP D 701 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C2' ATP E 702 " pdb=" C1' ATP E 702 " pdb=" C3' ATP E 702 " pdb=" O2' ATP E 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" C2' ATP B 702 " pdb=" C1' ATP B 702 " pdb=" C3' ATP B 702 " pdb=" O2' ATP B 702 " both_signs ideal model delta sigma weight residual False -2.68 -2.38 -0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 4393 not shown) Planarity restraints: 5077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 588 " -0.814 9.50e-02 1.11e+02 3.65e-01 8.09e+01 pdb=" NE ARG F 588 " 0.049 2.00e-02 2.50e+03 pdb=" CZ ARG F 588 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 588 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG F 588 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 588 " 0.741 9.50e-02 1.11e+02 3.32e-01 6.72e+01 pdb=" NE ARG B 588 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG B 588 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG B 588 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 588 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 588 " 0.667 9.50e-02 1.11e+02 2.99e-01 5.44e+01 pdb=" NE ARG D 588 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG D 588 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG D 588 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 588 " 0.021 2.00e-02 2.50e+03 ... (remaining 5074 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 321 2.56 - 3.14: 23164 3.14 - 3.73: 48888 3.73 - 4.31: 61824 4.31 - 4.90: 104332 Nonbonded interactions: 238529 Sorted by model distance: nonbonded pdb=" OD1 ASP D 533 " pdb="MG MG D 703 " model vdw 1.971 2.170 nonbonded pdb=" OD1 ASP F 533 " pdb="MG MG F 703 " model vdw 2.028 2.170 nonbonded pdb=" NE2 HIS D 448 " pdb="MG MG D 703 " model vdw 2.042 2.250 nonbonded pdb=" NE2 HIS C 245 " pdb="MG MG C 703 " model vdw 2.056 2.250 nonbonded pdb=" NE2 HIS A 243 " pdb="MG MG A 703 " model vdw 2.080 2.250 ... (remaining 238524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 272 or (resid 273 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 274 through 600 or resid 701 thro \ ugh 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 600 or resid 701 thro \ ugh 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 600 or resid 701 or ( \ resid 702 and (name O1A or name O1B or name O1G or name O2A or name O2B or name \ O2G or name O3A or name O3B or name O3G or name O5' or name PA or name PB or nam \ e PG )) or resid 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: 16.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.360 Check model and map are aligned: 0.260 Set scattering table: 0.300 Process input model: 72.210 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.180 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:3.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.233 29256 Z= 0.565 Angle : 0.750 16.880 39722 Z= 0.495 Chirality : 0.043 0.306 4396 Planarity : 0.009 0.365 5077 Dihedral : 18.809 89.435 10970 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP C 157 HIS 0.006 0.001 HIS F 21 PHE 0.015 0.001 PHE F 585 TYR 0.014 0.001 TYR B 77 ARG 0.005 0.000 ARG F 346 Details of bonding type rmsd hydrogen bonds : bond 0.15609 ( 1284) hydrogen bonds : angle 6.14267 ( 3696) covalent geometry : bond 0.00736 (29256) covalent geometry : angle 0.74996 (39722) *********************** 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 : 3.265 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: 0.3961 time to fit residues: 93.9958 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 : 3.254 ------------------------------------------------------------------------------- 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 301 optimal weight: 9.9990 chunk 270 optimal weight: 6.9990 chunk 150 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 279 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 170 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 324 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 HIS ** A 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN A 356 ASN A 406 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 ASN C 111 GLN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 145 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 GLN ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 353 GLN F 377 ASN F 406 GLN F 460 GLN F 500 ASN ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.039326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.026830 restraints weight = 249432.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.027747 restraints weight = 159419.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.028331 restraints weight = 123272.819| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 29256 Z= 0.250 Angle : 0.663 11.285 39722 Z= 0.341 Chirality : 0.043 0.187 4396 Planarity : 0.005 0.060 5077 Dihedral : 10.060 89.585 4191 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.76 % Favored : 94.10 % Rotamer: Outliers : 3.61 % Allowed : 28.78 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3558 helix: 1.54 (0.13), residues: 1719 sheet: 0.05 (0.25), residues: 447 loop : -1.14 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 221 HIS 0.006 0.001 HIS E 396 PHE 0.019 0.002 PHE F 585 TYR 0.019 0.002 TYR B 373 ARG 0.005 0.001 ARG B 558 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1284) hydrogen bonds : angle 4.66813 ( 3696) covalent geometry : bond 0.00528 (29256) covalent geometry : angle 0.66306 (39722) *********************** 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 219 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 108 time to evaluate : 3.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8740 (mmm) cc_final: 0.8446 (mmm) REVERT: A 106 MET cc_start: 0.9332 (pmm) cc_final: 0.9033 (pmm) REVERT: A 107 SER cc_start: 0.9566 (OUTLIER) cc_final: 0.9200 (p) REVERT: B 196 MET cc_start: 0.8889 (tpp) cc_final: 0.8632 (tpp) REVERT: B 265 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.9120 (pm20) REVERT: B 483 MET cc_start: 0.9314 (mtp) cc_final: 0.9075 (mtm) REVERT: B 494 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8427 (pt0) REVERT: B 531 ASN cc_start: 0.9435 (OUTLIER) cc_final: 0.8762 (m-40) REVERT: B 548 ILE cc_start: 0.9593 (OUTLIER) cc_final: 0.9384 (tp) REVERT: D 483 MET cc_start: 0.9117 (mtp) cc_final: 0.8838 (mtm) REVERT: E 320 GLN cc_start: 0.9373 (OUTLIER) cc_final: 0.9122 (tp-100) REVERT: E 404 MET cc_start: 0.9295 (ttp) cc_final: 0.8494 (tmm) REVERT: E 559 MET cc_start: 0.9221 (tpp) cc_final: 0.8843 (tpp) REVERT: F 494 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.8539 (pm20) outliers start: 111 outliers final: 30 residues processed: 211 average time/residue: 0.3643 time to fit residues: 128.4015 Evaluate side-chains 142 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 105 time to evaluate : 3.229 ------------------------------------------------------------------------------- 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 393 ILE 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 259 VAL Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 531 ASN Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 134 ILE 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 303 LYS 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 320 GLN Chi-restraints excluded: chain E residue 321 SER Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 494 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 255 optimal weight: 6.9990 chunk 99 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 268 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 313 optimal weight: 0.0270 chunk 178 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 chunk 25 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 314 GLN ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 ASN E 343 ASN E 396 HIS ** E 531 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.039744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.026962 restraints weight = 243274.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.027896 restraints weight = 157578.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.028496 restraints weight = 122192.458| |-----------------------------------------------------------------------------| r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2878 r_free = 0.2878 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29256 Z= 0.122 Angle : 0.550 10.371 39722 Z= 0.279 Chirality : 0.041 0.182 4396 Planarity : 0.003 0.051 5077 Dihedral : 9.565 88.641 4178 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.95 % Favored : 94.91 % Rotamer: Outliers : 2.86 % Allowed : 28.62 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.15), residues: 3558 helix: 1.75 (0.13), residues: 1719 sheet: 0.00 (0.25), residues: 453 loop : -1.05 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 157 HIS 0.008 0.001 HIS E 21 PHE 0.025 0.001 PHE B 208 TYR 0.015 0.001 TYR B 153 ARG 0.003 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 1284) hydrogen bonds : angle 4.40268 ( 3696) covalent geometry : bond 0.00269 (29256) covalent geometry : angle 0.54981 (39722) *********************** 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 192 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 104 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8860 (ttt) cc_final: 0.8631 (ttm) REVERT: A 89 MET cc_start: 0.8715 (mmm) cc_final: 0.8372 (mmm) REVERT: A 205 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.8012 (mm-40) REVERT: A 291 ASP cc_start: 0.9769 (t0) cc_final: 0.9506 (p0) REVERT: A 294 MET cc_start: 0.9197 (mmm) cc_final: 0.8992 (mmm) REVERT: B 14 MET cc_start: 0.8321 (mpp) cc_final: 0.8117 (mpp) REVERT: B 89 MET cc_start: 0.8851 (mtp) cc_final: 0.8554 (mpp) REVERT: B 196 MET cc_start: 0.8991 (tpp) cc_final: 0.8563 (tpp) REVERT: B 483 MET cc_start: 0.9325 (mtp) cc_final: 0.9016 (mtm) REVERT: B 485 THR cc_start: 0.9551 (OUTLIER) cc_final: 0.9284 (p) REVERT: B 494 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8362 (pt0) REVERT: B 531 ASN cc_start: 0.9458 (OUTLIER) cc_final: 0.8795 (m-40) REVERT: B 548 ILE cc_start: 0.9589 (OUTLIER) cc_final: 0.9356 (tp) REVERT: C 14 MET cc_start: 0.8610 (ppp) cc_final: 0.8064 (ppp) REVERT: C 29 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.8980 (pm20) REVERT: C 80 MET cc_start: 0.8885 (mtm) cc_final: 0.8442 (mtm) REVERT: C 559 MET cc_start: 0.9598 (mmm) cc_final: 0.9329 (tpp) REVERT: D 291 ASP cc_start: 0.9843 (m-30) cc_final: 0.9523 (p0) REVERT: D 483 MET cc_start: 0.9146 (mtp) cc_final: 0.8838 (mtm) REVERT: E 257 ASP cc_start: 0.9711 (OUTLIER) cc_final: 0.9424 (p0) REVERT: E 404 MET cc_start: 0.9293 (ttp) cc_final: 0.8523 (tmm) REVERT: E 559 MET cc_start: 0.9222 (tpp) cc_final: 0.8885 (tpp) REVERT: F 208 PHE cc_start: 0.7769 (m-80) cc_final: 0.7396 (m-80) REVERT: F 515 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8759 (mm) REVERT: F 559 MET cc_start: 0.9349 (tpp) cc_final: 0.9002 (tpp) outliers start: 88 outliers final: 41 residues processed: 181 average time/residue: 0.5405 time to fit residues: 166.9051 Evaluate side-chains 151 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 5.123 ------------------------------------------------------------------------------- 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 157 TRP Chi-restraints excluded: chain A residue 205 GLN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 485 THR 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 3 ARG Chi-restraints excluded: chain C residue 29 GLU 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 183 SER Chi-restraints excluded: chain C residue 186 ILE 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 116 LEU Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 204 ASN Chi-restraints excluded: chain E residue 222 LEU Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 257 ASP Chi-restraints excluded: chain E residue 496 CYS Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 122 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 199 optimal weight: 0.0370 chunk 25 optimal weight: 8.9990 chunk 213 optimal weight: 0.9980 chunk 167 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 chunk 354 optimal weight: 3.9990 chunk 156 optimal weight: 10.0000 chunk 135 optimal weight: 0.0000 chunk 239 optimal weight: 0.7980 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 439 HIS ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS ** 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 = 0.3382 r_free = 0.3382 target = 0.039693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.027080 restraints weight = 252974.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.028059 restraints weight = 158861.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.028679 restraints weight = 121660.728| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 29256 Z= 0.110 Angle : 0.544 13.316 39722 Z= 0.274 Chirality : 0.041 0.194 4396 Planarity : 0.003 0.042 5077 Dihedral : 9.282 89.756 4177 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.37 % Favored : 94.49 % Rotamer: Outliers : 3.02 % Allowed : 28.20 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 3558 helix: 1.75 (0.13), residues: 1719 sheet: 0.07 (0.25), residues: 453 loop : -1.05 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 PHE 0.022 0.001 PHE B 208 TYR 0.012 0.001 TYR E 591 ARG 0.003 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.03166 ( 1284) hydrogen bonds : angle 4.25858 ( 3696) covalent geometry : bond 0.00248 (29256) covalent geometry : angle 0.54430 (39722) *********************** 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 195 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 102 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8825 (ttt) cc_final: 0.8564 (ttm) REVERT: A 291 ASP cc_start: 0.9762 (t0) cc_final: 0.9479 (p0) REVERT: A 294 MET cc_start: 0.9205 (mmm) cc_final: 0.8966 (mmm) REVERT: A 404 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8921 (ttm) REVERT: B 89 MET cc_start: 0.8851 (mtp) cc_final: 0.8533 (mpp) REVERT: B 494 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8501 (pt0) REVERT: B 548 ILE cc_start: 0.9580 (OUTLIER) cc_final: 0.9341 (tp) REVERT: C 14 MET cc_start: 0.8560 (ppp) cc_final: 0.7860 (ppp) REVERT: C 29 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: C 94 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9178 (mm) REVERT: C 580 MET cc_start: 0.9113 (tpp) cc_final: 0.8644 (mpp) REVERT: D 291 ASP cc_start: 0.9818 (m-30) cc_final: 0.9425 (p0) REVERT: D 294 MET cc_start: 0.9270 (mpp) cc_final: 0.8901 (mpp) REVERT: D 483 MET cc_start: 0.9169 (mtp) cc_final: 0.8948 (ttm) REVERT: E 359 PHE cc_start: 0.9626 (OUTLIER) cc_final: 0.9396 (m-10) REVERT: E 404 MET cc_start: 0.9255 (ttp) cc_final: 0.8509 (tmm) REVERT: E 559 MET cc_start: 0.9233 (tpp) cc_final: 0.8862 (tpp) REVERT: F 151 MET cc_start: 0.8498 (ppp) cc_final: 0.8069 (ppp) REVERT: F 208 PHE cc_start: 0.7734 (m-80) cc_final: 0.7381 (m-80) REVERT: F 515 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8752 (mm) REVERT: F 559 MET cc_start: 0.9370 (tpp) cc_final: 0.8999 (tpp) outliers start: 93 outliers final: 53 residues processed: 186 average time/residue: 0.3841 time to fit residues: 121.5664 Evaluate side-chains 162 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 102 time to evaluate : 3.722 ------------------------------------------------------------------------------- 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 B residue 163 LEU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 94 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 183 SER 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 44 VAL Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 580 MET Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 252 SER Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 509 MET 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 139 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 THR 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 337 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 chunk 279 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 242 optimal weight: 4.9990 chunk 104 optimal weight: 0.8980 chunk 102 optimal weight: 0.1980 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 0.0870 chunk 355 optimal weight: 0.9980 overall best weight: 1.0360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.039985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.027026 restraints weight = 245213.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.027955 restraints weight = 157920.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.028565 restraints weight = 122966.068| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29256 Z= 0.113 Angle : 0.551 14.458 39722 Z= 0.272 Chirality : 0.040 0.222 4396 Planarity : 0.003 0.038 5077 Dihedral : 9.023 88.952 4177 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.14 % Favored : 94.72 % Rotamer: Outliers : 3.05 % Allowed : 28.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 3558 helix: 1.80 (0.13), residues: 1719 sheet: 0.13 (0.25), residues: 453 loop : -1.03 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 PHE 0.025 0.001 PHE D 208 TYR 0.011 0.001 TYR B 153 ARG 0.003 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.03059 ( 1284) hydrogen bonds : angle 4.18717 ( 3696) covalent geometry : bond 0.00253 (29256) covalent geometry : angle 0.55078 (39722) *********************** 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 197 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 103 time to evaluate : 3.371 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 14 MET cc_start: 0.9025 (pmm) cc_final: 0.8760 (pmm) REVERT: A 80 MET cc_start: 0.8847 (ttt) cc_final: 0.8570 (ttm) REVERT: A 89 MET cc_start: 0.8904 (tpp) cc_final: 0.8194 (mmm) REVERT: A 107 SER cc_start: 0.9604 (OUTLIER) cc_final: 0.9336 (p) REVERT: A 291 ASP cc_start: 0.9764 (t0) cc_final: 0.9499 (p0) REVERT: A 294 MET cc_start: 0.9202 (mmm) cc_final: 0.8973 (mmm) REVERT: A 544 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8629 (pm20) REVERT: B 89 MET cc_start: 0.8889 (mtp) cc_final: 0.8606 (mpp) REVERT: B 196 MET cc_start: 0.9056 (tpp) cc_final: 0.8442 (tpp) REVERT: B 384 ARG cc_start: 0.4575 (OUTLIER) cc_final: 0.3046 (mtt180) REVERT: B 483 MET cc_start: 0.9405 (ttm) cc_final: 0.9171 (mtt) REVERT: B 494 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8390 (pt0) REVERT: B 531 ASN cc_start: 0.9464 (OUTLIER) cc_final: 0.8820 (m-40) REVERT: B 548 ILE cc_start: 0.9588 (OUTLIER) cc_final: 0.9345 (tp) REVERT: C 27 PHE cc_start: 0.8502 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: C 29 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8901 (mp0) REVERT: C 89 MET cc_start: 0.8908 (pmm) cc_final: 0.8697 (pmm) REVERT: C 94 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9206 (mm) REVERT: C 106 MET cc_start: 0.8980 (pmm) cc_final: 0.8596 (pmm) REVERT: D 1 MET cc_start: 0.8261 (tmm) cc_final: 0.7968 (tmm) REVERT: D 3 ARG cc_start: 0.9276 (OUTLIER) cc_final: 0.8770 (mtm110) REVERT: D 291 ASP cc_start: 0.9816 (m-30) cc_final: 0.9614 (p0) REVERT: E 359 PHE cc_start: 0.9635 (OUTLIER) cc_final: 0.9397 (m-10) REVERT: E 404 MET cc_start: 0.9250 (ttp) cc_final: 0.8506 (tmm) REVERT: E 559 MET cc_start: 0.9243 (tpp) cc_final: 0.8862 (tpp) REVERT: F 151 MET cc_start: 0.8652 (ppp) cc_final: 0.8224 (ppp) REVERT: F 208 PHE cc_start: 0.7767 (m-80) cc_final: 0.7434 (m-80) REVERT: F 515 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8773 (mm) REVERT: F 559 MET cc_start: 0.9335 (tpp) cc_final: 0.8959 (tpp) outliers start: 94 outliers final: 55 residues processed: 187 average time/residue: 0.4385 time to fit residues: 136.2709 Evaluate side-chains 170 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 103 time to evaluate : 3.483 ------------------------------------------------------------------------------- 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 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG 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 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 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 183 SER Chi-restraints excluded: chain C residue 191 SER Chi-restraints excluded: chain C residue 359 PHE Chi-restraints excluded: chain C residue 384 ARG Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 116 LEU 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 222 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 509 MET Chi-restraints excluded: chain E residue 598 ILE Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 125 VAL Chi-restraints excluded: chain F residue 139 ASP Chi-restraints excluded: chain F residue 189 ILE Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 267 ASP Chi-restraints excluded: chain F residue 359 PHE Chi-restraints excluded: chain F residue 381 ILE Chi-restraints excluded: chain F residue 494 GLU Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 515 LEU 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 196 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 148 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 223 optimal weight: 0.7980 chunk 349 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 179 optimal weight: 0.4980 chunk 286 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 ASN ** C 177 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** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.040086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.027153 restraints weight = 245359.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.028104 restraints weight = 156675.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028708 restraints weight = 121429.709| |-----------------------------------------------------------------------------| r_work (final): 0.2891 ------------------------------------------------------------------------------- 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 = 0.74 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 = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 29256 Z= 0.104 Angle : 0.552 12.585 39722 Z= 0.271 Chirality : 0.040 0.188 4396 Planarity : 0.003 0.037 5077 Dihedral : 8.882 89.726 4177 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.17 % Favored : 94.72 % Rotamer: Outliers : 2.79 % Allowed : 28.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.15), residues: 3558 helix: 1.86 (0.13), residues: 1701 sheet: 0.18 (0.26), residues: 453 loop : -1.01 (0.17), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.006 0.001 HIS F 21 PHE 0.019 0.001 PHE D 208 TYR 0.010 0.001 TYR B 77 ARG 0.003 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 1284) hydrogen bonds : angle 4.13557 ( 3696) covalent geometry : bond 0.00231 (29256) covalent geometry : angle 0.55210 (39722) *********************** 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 188 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 102 time to evaluate : 3.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9017 (pmm) cc_final: 0.8750 (pmm) REVERT: A 80 MET cc_start: 0.8832 (ttt) cc_final: 0.8572 (ttm) REVERT: A 89 MET cc_start: 0.8920 (tpp) cc_final: 0.8301 (mmm) REVERT: A 291 ASP cc_start: 0.9759 (t0) cc_final: 0.9492 (p0) REVERT: A 294 MET cc_start: 0.9203 (mmm) cc_final: 0.8955 (mmm) REVERT: A 544 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.8618 (pm20) REVERT: B 89 MET cc_start: 0.8880 (mtp) cc_final: 0.8624 (mpp) REVERT: B 151 MET cc_start: 0.8571 (ttm) cc_final: 0.8268 (mpp) REVERT: B 384 ARG cc_start: 0.4550 (OUTLIER) cc_final: 0.3900 (mtm180) REVERT: B 483 MET cc_start: 0.9427 (ttm) cc_final: 0.9119 (mtt) REVERT: B 494 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8384 (pt0) REVERT: B 531 ASN cc_start: 0.9468 (OUTLIER) cc_final: 0.8838 (m-40) REVERT: B 548 ILE cc_start: 0.9590 (OUTLIER) cc_final: 0.9347 (tp) REVERT: C 27 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: C 94 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9213 (mm) REVERT: C 149 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8770 (mm) REVERT: C 559 MET cc_start: 0.9601 (mmm) cc_final: 0.9252 (tpp) REVERT: C 580 MET cc_start: 0.9084 (tpp) cc_final: 0.8727 (mpp) REVERT: D 3 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8769 (mtm110) REVERT: D 291 ASP cc_start: 0.9822 (m-30) cc_final: 0.9508 (p0) REVERT: D 483 MET cc_start: 0.9192 (ttm) cc_final: 0.8952 (mtt) REVERT: E 359 PHE cc_start: 0.9634 (OUTLIER) cc_final: 0.9391 (m-10) REVERT: E 404 MET cc_start: 0.9235 (ttp) cc_final: 0.8544 (tmm) REVERT: E 559 MET cc_start: 0.9251 (tpp) cc_final: 0.8868 (tpp) REVERT: F 208 PHE cc_start: 0.7745 (m-80) cc_final: 0.7420 (m-80) REVERT: F 515 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8783 (mm) REVERT: F 559 MET cc_start: 0.9353 (tpp) cc_final: 0.8990 (tpp) outliers start: 86 outliers final: 62 residues processed: 183 average time/residue: 0.3833 time to fit residues: 118.7043 Evaluate side-chains 175 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 102 time to evaluate : 3.249 ------------------------------------------------------------------------------- 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 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG 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 B residue 563 THR Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 75 GLU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 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 183 SER 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 522 LEU 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 390 LEU Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 596 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 222 LEU 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 509 MET 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 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 515 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 141 optimal weight: 0.1980 chunk 274 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 186 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.039525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.026504 restraints weight = 247460.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.027439 restraints weight = 160712.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.028028 restraints weight = 125657.711| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2858 r_free = 0.2858 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29256 Z= 0.139 Angle : 0.565 11.239 39722 Z= 0.280 Chirality : 0.040 0.187 4396 Planarity : 0.003 0.040 5077 Dihedral : 8.701 88.930 4177 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.34 % Favored : 94.55 % Rotamer: Outliers : 3.09 % Allowed : 27.94 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3558 helix: 1.91 (0.13), residues: 1704 sheet: 0.15 (0.25), residues: 465 loop : -0.98 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 PHE 0.023 0.001 PHE D 208 TYR 0.011 0.001 TYR B 153 ARG 0.004 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.03042 ( 1284) hydrogen bonds : angle 4.14048 ( 3696) covalent geometry : bond 0.00309 (29256) covalent geometry : angle 0.56497 (39722) *********************** 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 197 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 102 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 MET cc_start: 0.8902 (ttt) cc_final: 0.8693 (ttm) REVERT: A 89 MET cc_start: 0.8956 (tpp) cc_final: 0.8220 (mmm) REVERT: A 107 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.9365 (p) REVERT: A 291 ASP cc_start: 0.9758 (t0) cc_final: 0.9504 (p0) REVERT: A 294 MET cc_start: 0.9257 (mmm) cc_final: 0.9033 (mmm) REVERT: A 485 THR cc_start: 0.9718 (OUTLIER) cc_final: 0.9430 (t) REVERT: A 544 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.8712 (pm20) REVERT: B 89 MET cc_start: 0.8935 (mtp) cc_final: 0.8657 (mpp) REVERT: B 151 MET cc_start: 0.8675 (ttm) cc_final: 0.8439 (mpp) REVERT: B 196 MET cc_start: 0.9064 (tpp) cc_final: 0.8382 (tpp) REVERT: B 384 ARG cc_start: 0.4607 (OUTLIER) cc_final: 0.3961 (mtm180) REVERT: B 483 MET cc_start: 0.9436 (ttm) cc_final: 0.9119 (mtt) REVERT: B 494 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8566 (pt0) REVERT: B 548 ILE cc_start: 0.9597 (OUTLIER) cc_final: 0.9357 (tp) REVERT: C 27 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: C 29 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8813 (mp0) REVERT: C 94 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9237 (mm) REVERT: C 106 MET cc_start: 0.8955 (pmm) cc_final: 0.8449 (pmm) REVERT: C 559 MET cc_start: 0.9633 (mmm) cc_final: 0.9349 (tpp) REVERT: D 1 MET cc_start: 0.8307 (tmm) cc_final: 0.8055 (tmm) REVERT: D 3 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8751 (mtm110) REVERT: D 291 ASP cc_start: 0.9826 (m-30) cc_final: 0.9411 (p0) REVERT: D 294 MET cc_start: 0.9360 (mpp) cc_final: 0.8863 (mpp) REVERT: D 483 MET cc_start: 0.9207 (ttm) cc_final: 0.8953 (mtt) REVERT: E 151 MET cc_start: 0.8053 (mtt) cc_final: 0.7230 (tmm) REVERT: E 359 PHE cc_start: 0.9667 (OUTLIER) cc_final: 0.9437 (m-10) REVERT: E 404 MET cc_start: 0.9230 (ttp) cc_final: 0.8639 (tmm) REVERT: E 559 MET cc_start: 0.9298 (tpp) cc_final: 0.8852 (tpp) REVERT: F 404 MET cc_start: 0.9111 (tpp) cc_final: 0.8870 (tpp) REVERT: F 421 PHE cc_start: 0.6859 (OUTLIER) cc_final: 0.6360 (p90) REVERT: F 515 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8802 (mm) outliers start: 95 outliers final: 63 residues processed: 191 average time/residue: 0.4305 time to fit residues: 137.2576 Evaluate side-chains 177 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 101 time to evaluate : 3.778 ------------------------------------------------------------------------------- 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 205 GLN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 544 GLU 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 175 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 528 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 563 THR Chi-restraints excluded: chain C residue 3 ARG Chi-restraints excluded: chain C residue 27 PHE Chi-restraints excluded: chain C residue 29 GLU Chi-restraints excluded: chain C residue 94 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 183 SER 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 438 VAL Chi-restraints excluded: chain C residue 522 LEU 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 116 LEU Chi-restraints excluded: chain D residue 189 ILE 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 509 MET 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 267 ASP 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 495 MET Chi-restraints excluded: chain F residue 511 ASN Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 563 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 273 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 291 optimal weight: 0.0030 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 320 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.039650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.026701 restraints weight = 246145.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.027634 restraints weight = 160331.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.028227 restraints weight = 125192.218| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29256 Z= 0.122 Angle : 0.563 13.540 39722 Z= 0.275 Chirality : 0.040 0.183 4396 Planarity : 0.003 0.037 5077 Dihedral : 8.585 89.799 4177 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.66 % Rotamer: Outliers : 2.96 % Allowed : 28.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3558 helix: 1.92 (0.13), residues: 1704 sheet: 0.12 (0.25), residues: 459 loop : -0.96 (0.18), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 PHE 0.023 0.001 PHE F 208 TYR 0.010 0.001 TYR B 77 ARG 0.003 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.02970 ( 1284) hydrogen bonds : angle 4.06737 ( 3696) covalent geometry : bond 0.00272 (29256) covalent geometry : angle 0.56314 (39722) *********************** 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 192 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 101 time to evaluate : 3.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9072 (pmm) cc_final: 0.8804 (pmm) REVERT: A 80 MET cc_start: 0.8894 (ttt) cc_final: 0.8678 (ttm) REVERT: A 89 MET cc_start: 0.8962 (tpp) cc_final: 0.8245 (mmm) REVERT: A 107 SER cc_start: 0.9646 (OUTLIER) cc_final: 0.9406 (p) REVERT: A 291 ASP cc_start: 0.9754 (t0) cc_final: 0.9504 (p0) REVERT: A 294 MET cc_start: 0.9254 (mmm) cc_final: 0.9022 (mmm) REVERT: A 485 THR cc_start: 0.9725 (OUTLIER) cc_final: 0.9446 (t) REVERT: A 544 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.8708 (pm20) REVERT: B 89 MET cc_start: 0.8909 (mtp) cc_final: 0.8650 (mpp) REVERT: B 106 MET cc_start: 0.8789 (ptp) cc_final: 0.8439 (ptp) REVERT: B 384 ARG cc_start: 0.4673 (OUTLIER) cc_final: 0.4049 (mtm180) REVERT: B 483 MET cc_start: 0.9437 (ttm) cc_final: 0.9123 (mtt) REVERT: B 494 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8406 (pt0) REVERT: B 531 ASN cc_start: 0.9450 (OUTLIER) cc_final: 0.8818 (m-40) REVERT: B 548 ILE cc_start: 0.9596 (OUTLIER) cc_final: 0.9357 (tp) REVERT: C 27 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.8276 (m-80) REVERT: C 29 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8858 (mp0) REVERT: C 94 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9235 (mm) REVERT: C 106 MET cc_start: 0.8937 (pmm) cc_final: 0.8394 (pmm) REVERT: C 559 MET cc_start: 0.9622 (mmm) cc_final: 0.9308 (tpp) REVERT: D 1 MET cc_start: 0.8302 (tmm) cc_final: 0.7866 (tmm) REVERT: D 3 ARG cc_start: 0.9254 (OUTLIER) cc_final: 0.8635 (mtm110) REVERT: D 291 ASP cc_start: 0.9825 (m-30) cc_final: 0.9514 (p0) REVERT: D 483 MET cc_start: 0.9214 (ttm) cc_final: 0.8870 (mtt) REVERT: E 14 MET cc_start: 0.8917 (tpt) cc_final: 0.8265 (tpp) REVERT: E 359 PHE cc_start: 0.9678 (OUTLIER) cc_final: 0.9441 (m-10) REVERT: E 404 MET cc_start: 0.9253 (ttp) cc_final: 0.8667 (tmm) REVERT: E 559 MET cc_start: 0.9299 (tpp) cc_final: 0.8846 (tpp) REVERT: F 404 MET cc_start: 0.9104 (tpp) cc_final: 0.8880 (tpp) REVERT: F 421 PHE cc_start: 0.6871 (OUTLIER) cc_final: 0.6442 (p90) REVERT: F 515 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8822 (mm) REVERT: F 580 MET cc_start: 0.9077 (mmm) cc_final: 0.8062 (mmm) outliers start: 91 outliers final: 63 residues processed: 184 average time/residue: 0.3702 time to fit residues: 115.7604 Evaluate side-chains 177 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 100 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 544 GLU 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 175 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 526 ILE 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 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 75 GLU Chi-restraints excluded: chain C residue 94 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 183 SER 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 438 VAL Chi-restraints excluded: chain C residue 522 LEU Chi-restraints excluded: chain C residue 528 VAL Chi-restraints excluded: chain D residue 3 ARG Chi-restraints excluded: chain D residue 29 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 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 496 CYS Chi-restraints excluded: chain E residue 509 MET 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 359 PHE Chi-restraints excluded: chain F residue 381 ILE 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 495 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 THR 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 297 optimal weight: 9.9990 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 230 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 140 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 309 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 HIS ** 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 = 0.3362 r_free = 0.3362 target = 0.038377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.026373 restraints weight = 248613.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.027323 restraints weight = 156786.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.027925 restraints weight = 120763.631| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.027 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29256 Z= 0.142 Angle : 0.582 12.834 39722 Z= 0.283 Chirality : 0.040 0.194 4396 Planarity : 0.003 0.038 5077 Dihedral : 8.482 89.883 4177 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 2.70 % Allowed : 28.30 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 3558 helix: 1.94 (0.13), residues: 1710 sheet: 0.03 (0.25), residues: 477 loop : -1.00 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS B 124 PHE 0.023 0.001 PHE D 208 TYR 0.012 0.001 TYR D 153 ARG 0.004 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 1284) hydrogen bonds : angle 4.08566 ( 3696) covalent geometry : bond 0.00315 (29256) covalent geometry : angle 0.58239 (39722) *********************** 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 183 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 100 time to evaluate : 3.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9072 (pmm) cc_final: 0.8802 (pmm) REVERT: A 80 MET cc_start: 0.8893 (ttt) cc_final: 0.8669 (ttm) REVERT: A 89 MET cc_start: 0.8976 (tpp) cc_final: 0.8251 (mmm) REVERT: A 107 SER cc_start: 0.9640 (OUTLIER) cc_final: 0.9413 (p) REVERT: A 291 ASP cc_start: 0.9749 (t0) cc_final: 0.9495 (p0) REVERT: A 294 MET cc_start: 0.9281 (mmm) cc_final: 0.9031 (mmm) REVERT: A 544 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8700 (pm20) REVERT: B 106 MET cc_start: 0.8865 (ptp) cc_final: 0.8508 (ptp) REVERT: B 196 MET cc_start: 0.8949 (tpp) cc_final: 0.8191 (tpp) REVERT: B 384 ARG cc_start: 0.4743 (OUTLIER) cc_final: 0.4132 (mtm180) REVERT: B 483 MET cc_start: 0.9454 (ttm) cc_final: 0.9225 (mtm) REVERT: B 494 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8468 (pt0) REVERT: B 531 ASN cc_start: 0.9443 (OUTLIER) cc_final: 0.8818 (m-40) REVERT: B 548 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9356 (tp) REVERT: C 27 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.8292 (m-80) REVERT: C 29 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8862 (mp0) REVERT: C 94 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9253 (mm) REVERT: C 106 MET cc_start: 0.8942 (pmm) cc_final: 0.8387 (pmm) REVERT: C 559 MET cc_start: 0.9625 (mmm) cc_final: 0.9330 (tpp) REVERT: D 1 MET cc_start: 0.8312 (tmm) cc_final: 0.7821 (tmm) REVERT: D 3 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8746 (mtm110) REVERT: D 291 ASP cc_start: 0.9826 (m-30) cc_final: 0.9499 (p0) REVERT: D 483 MET cc_start: 0.9227 (ttm) cc_final: 0.8859 (mtt) REVERT: E 359 PHE cc_start: 0.9689 (OUTLIER) cc_final: 0.9463 (m-10) REVERT: E 404 MET cc_start: 0.9260 (ttp) cc_final: 0.8709 (tmm) REVERT: E 559 MET cc_start: 0.9335 (tpp) cc_final: 0.8868 (tpp) REVERT: F 421 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6340 (p90) REVERT: F 515 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8884 (mm) outliers start: 83 outliers final: 63 residues processed: 178 average time/residue: 0.3886 time to fit residues: 116.7175 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 : 3.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 GLN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 526 ILE 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 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 75 GLU Chi-restraints excluded: chain C residue 94 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 183 SER 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 438 VAL Chi-restraints excluded: chain C residue 522 LEU 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 390 LEU Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 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 496 CYS Chi-restraints excluded: chain E residue 509 MET 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 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 495 MET Chi-restraints excluded: chain F residue 511 ASN Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 THR 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 82 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 chunk 176 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 276 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 74 optimal weight: 0.7980 chunk 262 optimal weight: 9.9990 chunk 211 optimal weight: 2.9990 chunk 352 optimal weight: 10.0000 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.038434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.026583 restraints weight = 245788.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.027523 restraints weight = 154539.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.028116 restraints weight = 118823.099| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- 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 = 0.71 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 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29256 Z= 0.124 Angle : 0.594 12.250 39722 Z= 0.288 Chirality : 0.040 0.186 4396 Planarity : 0.003 0.040 5077 Dihedral : 8.421 89.872 4177 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.34 % Favored : 94.58 % Rotamer: Outliers : 2.63 % Allowed : 28.36 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.15), residues: 3558 helix: 1.92 (0.13), residues: 1710 sheet: 0.05 (0.25), residues: 477 loop : -1.00 (0.18), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 PHE 0.024 0.001 PHE D 208 TYR 0.015 0.001 TYR D 153 ARG 0.004 0.000 ARG E 384 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 1284) hydrogen bonds : angle 4.05868 ( 3696) covalent geometry : bond 0.00278 (29256) covalent geometry : angle 0.59385 (39722) ********************** 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 182 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 101 time to evaluate : 5.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.9077 (pmm) cc_final: 0.8808 (pmm) REVERT: A 89 MET cc_start: 0.8983 (tpp) cc_final: 0.8263 (mmm) REVERT: A 107 SER cc_start: 0.9648 (OUTLIER) cc_final: 0.9362 (p) REVERT: A 291 ASP cc_start: 0.9751 (t0) cc_final: 0.9500 (p0) REVERT: A 294 MET cc_start: 0.9276 (mmm) cc_final: 0.9023 (mmm) REVERT: A 544 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8702 (pm20) REVERT: B 106 MET cc_start: 0.8885 (ptp) cc_final: 0.8539 (ptp) REVERT: B 196 MET cc_start: 0.9009 (tpp) cc_final: 0.8312 (tpp) REVERT: B 384 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.4253 (mtm180) REVERT: B 483 MET cc_start: 0.9451 (ttm) cc_final: 0.9224 (mtm) REVERT: B 494 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: B 531 ASN cc_start: 0.9426 (OUTLIER) cc_final: 0.8822 (m-40) REVERT: B 548 ILE cc_start: 0.9588 (OUTLIER) cc_final: 0.9348 (tp) REVERT: C 27 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.8274 (m-80) REVERT: C 29 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: C 94 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9232 (mm) REVERT: C 106 MET cc_start: 0.8923 (pmm) cc_final: 0.8372 (pmm) REVERT: C 559 MET cc_start: 0.9623 (mmm) cc_final: 0.9315 (tpp) REVERT: D 483 MET cc_start: 0.9232 (ttm) cc_final: 0.8855 (mtt) REVERT: E 359 PHE cc_start: 0.9689 (OUTLIER) cc_final: 0.9461 (m-10) REVERT: E 404 MET cc_start: 0.9261 (ttp) cc_final: 0.8738 (tmm) REVERT: E 559 MET cc_start: 0.9342 (tpp) cc_final: 0.8886 (tpp) REVERT: F 196 MET cc_start: 0.9286 (tpp) cc_final: 0.8838 (tpp) REVERT: F 404 MET cc_start: 0.9043 (tpp) cc_final: 0.8534 (mtt) REVERT: F 421 PHE cc_start: 0.6750 (OUTLIER) cc_final: 0.6332 (p90) REVERT: F 515 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8927 (mm) outliers start: 81 outliers final: 63 residues processed: 174 average time/residue: 0.4409 time to fit residues: 130.2020 Evaluate side-chains 175 residues out of total 3081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 100 time to evaluate : 3.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 GLN Chi-restraints excluded: chain A residue 310 CYS Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 448 HIS Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain B residue 359 PHE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 494 GLU Chi-restraints excluded: chain B residue 526 ILE 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 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 75 GLU Chi-restraints excluded: chain C residue 94 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 183 SER 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 438 VAL Chi-restraints excluded: chain C residue 522 LEU 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 116 LEU Chi-restraints excluded: chain D residue 217 ILE Chi-restraints excluded: chain D residue 303 LYS Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain D residue 563 THR Chi-restraints excluded: chain D residue 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 496 CYS Chi-restraints excluded: chain E residue 509 MET 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 267 ASP 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 495 MET Chi-restraints excluded: chain F residue 515 LEU Chi-restraints excluded: chain F residue 532 THR 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 81 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 350 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 251 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 284 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 354 optimal weight: 5.9990 chunk 321 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.038584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.026717 restraints weight = 245940.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027660 restraints weight = 154845.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028253 restraints weight = 119115.147| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 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 = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.028 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29256 Z= 0.112 Angle : 0.585 13.093 39722 Z= 0.284 Chirality : 0.040 0.183 4396 Planarity : 0.003 0.043 5077 Dihedral : 8.277 88.643 4177 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.28 % Favored : 94.63 % Rotamer: Outliers : 2.57 % Allowed : 28.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 3558 helix: 1.92 (0.13), residues: 1704 sheet: 0.07 (0.25), residues: 465 loop : -0.97 (0.18), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 157 HIS 0.005 0.001 HIS F 21 PHE 0.023 0.001 PHE D 208 TYR 0.015 0.001 TYR D 153 ARG 0.003 0.000 ARG A 3 Details of bonding type rmsd hydrogen bonds : bond 0.02950 ( 1284) hydrogen bonds : angle 4.02774 ( 3696) covalent geometry : bond 0.00254 (29256) covalent geometry : angle 0.58483 (39722) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9810.83 seconds wall clock time: 177 minutes 43.10 seconds (10663.10 seconds total)