Starting phenix.real_space_refine on Fri Sep 19 01:13:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efg_47972/09_2025/9efg_47972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efg_47972/09_2025/9efg_47972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9efg_47972/09_2025/9efg_47972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efg_47972/09_2025/9efg_47972.map" model { file = "/net/cci-nas-00/data/ceres_data/9efg_47972/09_2025/9efg_47972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efg_47972/09_2025/9efg_47972.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 48 5.16 5 C 13880 2.51 5 N 3428 2.21 5 O 4312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21669 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5417 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 20, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5417 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 20, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5417 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 20, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 5417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5417 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 20, 'TRANS': 656} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.47, per 1000 atoms: 0.25 Number of scatterers: 21669 At special positions: 0 Unit cell: (178.365, 178.365, 150.259, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 Mg 1 11.99 O 4312 8.00 N 3428 7.00 C 13880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 949.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 56 sheets defined 29.5% alpha, 22.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 99 through 181 Proline residue: A 117 - end of helix removed outlier: 3.815A pdb=" N GLU A 166 " --> pdb=" O SER A 162 " (cutoff:3.500A) Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 227 through 241 Processing helix chain 'A' and resid 248 through 259 removed outlier: 3.722A pdb=" N THR A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 297 Processing helix chain 'A' and resid 304 through 323 Processing helix chain 'A' and resid 324 through 327 removed outlier: 3.543A pdb=" N LEU A 327 " --> pdb=" O LEU A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 324 through 327' Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 514 through 523 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.900A pdb=" N TYR A 620 " --> pdb=" O ASN A 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 181 Proline residue: B 117 - end of helix removed outlier: 3.815A pdb=" N GLU B 166 " --> pdb=" O SER B 162 " (cutoff:3.500A) Proline residue: B 169 - end of helix Processing helix chain 'B' and resid 210 through 222 Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.721A pdb=" N THR B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 297 Processing helix chain 'B' and resid 304 through 323 Processing helix chain 'B' and resid 324 through 327 removed outlier: 3.544A pdb=" N LEU B 327 " --> pdb=" O LEU B 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 514 through 523 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.900A pdb=" N TYR B 620 " --> pdb=" O ASN B 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 181 Proline residue: C 117 - end of helix removed outlier: 3.815A pdb=" N GLU C 166 " --> pdb=" O SER C 162 " (cutoff:3.500A) Proline residue: C 169 - end of helix Processing helix chain 'C' and resid 210 through 222 Processing helix chain 'C' and resid 227 through 241 Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.721A pdb=" N THR C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 297 Processing helix chain 'C' and resid 304 through 323 Processing helix chain 'C' and resid 324 through 327 removed outlier: 3.544A pdb=" N LEU C 327 " --> pdb=" O LEU C 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 324 through 327' Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 514 through 523 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.900A pdb=" N TYR C 620 " --> pdb=" O ASN C 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 181 Proline residue: D 117 - end of helix removed outlier: 3.815A pdb=" N GLU D 166 " --> pdb=" O SER D 162 " (cutoff:3.500A) Proline residue: D 169 - end of helix Processing helix chain 'D' and resid 210 through 222 Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'D' and resid 248 through 259 removed outlier: 3.722A pdb=" N THR D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 297 Processing helix chain 'D' and resid 304 through 323 Processing helix chain 'D' and resid 324 through 327 removed outlier: 3.543A pdb=" N LEU D 327 " --> pdb=" O LEU D 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 327' Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 514 through 523 Processing helix chain 'D' and resid 616 through 620 removed outlier: 3.900A pdb=" N TYR D 620 " --> pdb=" O ASN D 617 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 330 through 331 removed outlier: 6.483A pdb=" N LYS A 512 " --> pdb=" O ASN A 494 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 338 removed outlier: 3.541A pdb=" N VAL A 337 " --> pdb=" O MET A 480 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.536A pdb=" N THR A 440 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 426 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU A 438 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE A 428 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG A 436 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 430 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU A 455 " --> pdb=" O PHE A 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.536A pdb=" N THR A 440 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE A 426 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU A 438 " --> pdb=" O ILE A 426 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE A 428 " --> pdb=" O ARG A 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG A 436 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS A 430 " --> pdb=" O ASN A 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS A 409 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR A 437 " --> pdb=" O LYS A 409 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.454A pdb=" N TYR A 374 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE A 361 " --> pdb=" O LYS A 372 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS A 372 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 501 removed outlier: 3.530A pdb=" N ILE A 506 " --> pdb=" O ASP A 501 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 557 through 558 Processing sheet with id=AA8, first strand: chain 'A' and resid 557 through 558 removed outlier: 3.645A pdb=" N LYS A 614 " --> pdb=" O HIS A 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 564 through 566 removed outlier: 3.874A pdb=" N VAL A 605 " --> pdb=" O GLN A 634 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN A 634 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 598 through 600 Processing sheet with id=AB2, first strand: chain 'A' and resid 689 through 691 Processing sheet with id=AB3, first strand: chain 'A' and resid 757 through 759 removed outlier: 3.781A pdb=" N PHE A 729 " --> pdb=" O VAL A 757 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 757 through 759 removed outlier: 3.781A pdb=" N PHE A 729 " --> pdb=" O VAL A 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 793 " --> pdb=" O ASN A 724 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER A 728 " --> pdb=" O ASP A 789 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP A 789 " --> pdb=" O SER A 728 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'B' and resid 330 through 331 removed outlier: 6.481A pdb=" N LYS B 512 " --> pdb=" O ASN B 494 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 335 through 338 removed outlier: 3.540A pdb=" N VAL B 337 " --> pdb=" O MET B 480 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.536A pdb=" N THR B 440 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE B 426 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU B 438 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 428 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG B 436 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS B 430 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU B 455 " --> pdb=" O PHE B 443 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.536A pdb=" N THR B 440 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE B 426 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU B 438 " --> pdb=" O ILE B 426 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE B 428 " --> pdb=" O ARG B 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG B 436 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS B 430 " --> pdb=" O ASN B 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN B 434 " --> pdb=" O LYS B 430 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS B 409 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR B 437 " --> pdb=" O LYS B 409 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 357 through 362 removed outlier: 6.454A pdb=" N TYR B 374 " --> pdb=" O VAL B 359 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N PHE B 361 " --> pdb=" O LYS B 372 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LYS B 372 " --> pdb=" O PHE B 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 499 through 501 removed outlier: 3.530A pdb=" N ILE B 506 " --> pdb=" O ASP B 501 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 557 through 558 Processing sheet with id=AC4, first strand: chain 'B' and resid 557 through 558 removed outlier: 3.645A pdb=" N LYS B 614 " --> pdb=" O HIS B 650 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 564 through 566 removed outlier: 3.875A pdb=" N VAL B 605 " --> pdb=" O GLN B 634 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN B 634 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 598 through 600 Processing sheet with id=AC7, first strand: chain 'B' and resid 689 through 691 Processing sheet with id=AC8, first strand: chain 'B' and resid 757 through 759 removed outlier: 3.780A pdb=" N PHE B 729 " --> pdb=" O VAL B 757 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 757 through 759 removed outlier: 3.780A pdb=" N PHE B 729 " --> pdb=" O VAL B 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS B 793 " --> pdb=" O ASN B 724 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER B 728 " --> pdb=" O ASP B 789 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP B 789 " --> pdb=" O SER B 728 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 330 through 331 removed outlier: 6.482A pdb=" N LYS C 512 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 335 through 338 removed outlier: 3.540A pdb=" N VAL C 337 " --> pdb=" O MET C 480 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 346 through 350 removed outlier: 6.537A pdb=" N THR C 440 " --> pdb=" O THR C 424 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 426 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU C 438 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE C 428 " --> pdb=" O ARG C 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG C 436 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS C 430 " --> pdb=" O ASN C 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU C 455 " --> pdb=" O PHE C 443 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 346 through 350 removed outlier: 6.537A pdb=" N THR C 440 " --> pdb=" O THR C 424 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE C 426 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU C 438 " --> pdb=" O ILE C 426 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE C 428 " --> pdb=" O ARG C 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG C 436 " --> pdb=" O PHE C 428 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS C 430 " --> pdb=" O ASN C 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN C 434 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS C 409 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N TYR C 437 " --> pdb=" O LYS C 409 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 357 through 362 removed outlier: 6.455A pdb=" N TYR C 374 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C 361 " --> pdb=" O LYS C 372 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS C 372 " --> pdb=" O PHE C 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 499 through 501 removed outlier: 3.529A pdb=" N ILE C 506 " --> pdb=" O ASP C 501 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 557 through 558 Processing sheet with id=AD9, first strand: chain 'C' and resid 557 through 558 removed outlier: 3.645A pdb=" N LYS C 614 " --> pdb=" O HIS C 650 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 564 through 566 removed outlier: 3.874A pdb=" N VAL C 605 " --> pdb=" O GLN C 634 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 634 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 598 through 600 Processing sheet with id=AE3, first strand: chain 'C' and resid 689 through 691 Processing sheet with id=AE4, first strand: chain 'C' and resid 757 through 759 removed outlier: 3.780A pdb=" N PHE C 729 " --> pdb=" O VAL C 757 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 757 through 759 removed outlier: 3.780A pdb=" N PHE C 729 " --> pdb=" O VAL C 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 793 " --> pdb=" O ASN C 724 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER C 728 " --> pdb=" O ASP C 789 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP C 789 " --> pdb=" O SER C 728 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE7, first strand: chain 'D' and resid 330 through 331 removed outlier: 6.481A pdb=" N LYS D 512 " --> pdb=" O ASN D 494 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 335 through 338 removed outlier: 3.541A pdb=" N VAL D 337 " --> pdb=" O MET D 480 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 346 through 350 removed outlier: 6.536A pdb=" N THR D 440 " --> pdb=" O THR D 424 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE D 426 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU D 438 " --> pdb=" O ILE D 426 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE D 428 " --> pdb=" O ARG D 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG D 436 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS D 430 " --> pdb=" O ASN D 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N GLU D 455 " --> pdb=" O PHE D 443 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 346 through 350 removed outlier: 6.536A pdb=" N THR D 440 " --> pdb=" O THR D 424 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ILE D 426 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLU D 438 " --> pdb=" O ILE D 426 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N PHE D 428 " --> pdb=" O ARG D 436 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ARG D 436 " --> pdb=" O PHE D 428 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS D 430 " --> pdb=" O ASN D 434 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N ASN D 434 " --> pdb=" O LYS D 430 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS D 409 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N TYR D 437 " --> pdb=" O LYS D 409 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.455A pdb=" N TYR D 374 " --> pdb=" O VAL D 359 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE D 361 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS D 372 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 499 through 501 removed outlier: 3.530A pdb=" N ILE D 506 " --> pdb=" O ASP D 501 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 557 through 558 Processing sheet with id=AF5, first strand: chain 'D' and resid 557 through 558 removed outlier: 3.645A pdb=" N LYS D 614 " --> pdb=" O HIS D 650 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 564 through 566 removed outlier: 3.876A pdb=" N VAL D 605 " --> pdb=" O GLN D 634 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN D 634 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 598 through 600 Processing sheet with id=AF8, first strand: chain 'D' and resid 689 through 691 Processing sheet with id=AF9, first strand: chain 'D' and resid 757 through 759 removed outlier: 3.780A pdb=" N PHE D 729 " --> pdb=" O VAL D 757 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 757 through 759 removed outlier: 3.780A pdb=" N PHE D 729 " --> pdb=" O VAL D 757 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS D 793 " --> pdb=" O ASN D 724 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N SER D 728 " --> pdb=" O ASP D 789 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ASP D 789 " --> pdb=" O SER D 728 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 734 through 736 956 hydrogen bonds defined for protein. 2616 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: 4.55 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6914 1.34 - 1.46: 4395 1.46 - 1.58: 10719 1.58 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 22104 Sorted by residual: bond pdb=" N ILE C 485 " pdb=" CA ILE C 485 " ideal model delta sigma weight residual 1.474 1.457 0.017 1.57e-02 4.06e+03 1.16e+00 bond pdb=" N ILE A 485 " pdb=" CA ILE A 485 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.10e+00 bond pdb=" N ILE B 485 " pdb=" CA ILE B 485 " ideal model delta sigma weight residual 1.474 1.458 0.016 1.57e-02 4.06e+03 1.08e+00 bond pdb=" N ILE D 485 " pdb=" CA ILE D 485 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.02e+00 bond pdb=" CA PRO D 325 " pdb=" CB PRO D 325 " ideal model delta sigma weight residual 1.532 1.537 -0.006 7.10e-03 1.98e+04 6.55e-01 ... (remaining 22099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 29203 1.16 - 2.31: 579 2.31 - 3.47: 118 3.47 - 4.63: 8 4.63 - 5.78: 32 Bond angle restraints: 29940 Sorted by residual: angle pdb=" N THR B 326 " pdb=" CA THR B 326 " pdb=" C THR B 326 " ideal model delta sigma weight residual 114.62 109.42 5.20 1.14e+00 7.69e-01 2.08e+01 angle pdb=" N THR A 326 " pdb=" CA THR A 326 " pdb=" C THR A 326 " ideal model delta sigma weight residual 114.62 109.44 5.18 1.14e+00 7.69e-01 2.06e+01 angle pdb=" N THR C 326 " pdb=" CA THR C 326 " pdb=" C THR C 326 " ideal model delta sigma weight residual 114.62 109.47 5.15 1.14e+00 7.69e-01 2.04e+01 angle pdb=" N THR D 326 " pdb=" CA THR D 326 " pdb=" C THR D 326 " ideal model delta sigma weight residual 114.62 109.47 5.15 1.14e+00 7.69e-01 2.04e+01 angle pdb=" C ASN D 627 " pdb=" CA ASN D 627 " pdb=" CB ASN D 627 " ideal model delta sigma weight residual 115.89 110.23 5.66 1.32e+00 5.74e-01 1.84e+01 ... (remaining 29935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.22: 12393 13.22 - 26.45: 650 26.45 - 39.67: 163 39.67 - 52.89: 44 52.89 - 66.11: 8 Dihedral angle restraints: 13258 sinusoidal: 5270 harmonic: 7988 Sorted by residual: dihedral pdb=" CA ILE B 611 " pdb=" CB ILE B 611 " pdb=" CG1 ILE B 611 " pdb=" CD1 ILE B 611 " ideal model delta sinusoidal sigma weight residual 180.00 122.97 57.03 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ILE C 611 " pdb=" CB ILE C 611 " pdb=" CG1 ILE C 611 " pdb=" CD1 ILE C 611 " ideal model delta sinusoidal sigma weight residual 180.00 123.02 56.98 3 1.50e+01 4.44e-03 9.42e+00 dihedral pdb=" CA ILE A 611 " pdb=" CB ILE A 611 " pdb=" CG1 ILE A 611 " pdb=" CD1 ILE A 611 " ideal model delta sinusoidal sigma weight residual 180.00 123.05 56.95 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 13255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2170 0.026 - 0.053: 710 0.053 - 0.079: 236 0.079 - 0.106: 190 0.106 - 0.132: 82 Chirality restraints: 3388 Sorted by residual: chirality pdb=" CA ILE A 426 " pdb=" N ILE A 426 " pdb=" C ILE A 426 " pdb=" CB ILE A 426 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE D 600 " pdb=" N ILE D 600 " pdb=" C ILE D 600 " pdb=" CB ILE D 600 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA ILE B 600 " pdb=" N ILE B 600 " pdb=" C ILE B 600 " pdb=" CB ILE B 600 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 ... (remaining 3385 not shown) Planarity restraints: 3828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 534 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO C 535 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO C 535 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 535 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 534 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO B 535 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 535 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 535 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO D 534 " 0.018 5.00e-02 4.00e+02 2.67e-02 1.14e+00 pdb=" N PRO D 535 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO D 535 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO D 535 " 0.015 5.00e-02 4.00e+02 ... (remaining 3825 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2169 2.75 - 3.29: 22044 3.29 - 3.83: 36524 3.83 - 4.36: 41931 4.36 - 4.90: 74384 Nonbonded interactions: 177052 Sorted by model distance: nonbonded pdb=" OE1 GLU D 362 " pdb=" OH TYR D 374 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU C 362 " pdb=" OH TYR C 374 " model vdw 2.214 3.040 nonbonded pdb=" OE1 GLU A 362 " pdb=" OH TYR A 374 " model vdw 2.215 3.040 nonbonded pdb=" OE1 GLU B 362 " pdb=" OH TYR B 374 " model vdw 2.215 3.040 nonbonded pdb=" OG SER A 162 " pdb=" ND2 ASN B 161 " model vdw 2.302 3.120 ... (remaining 177047 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 98 through 797) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.950 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.030 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.002 0.021 22104 Z= 0.091 Angle : 0.444 5.785 29940 Z= 0.251 Chirality : 0.039 0.132 3388 Planarity : 0.003 0.027 3828 Dihedral : 9.058 66.115 8114 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.13 % Favored : 93.72 % Rotamer: Outliers : 2.61 % Allowed : 6.04 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.17), residues: 2692 helix: 4.15 (0.17), residues: 736 sheet: -1.02 (0.21), residues: 700 loop : -2.05 (0.16), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 436 TYR 0.006 0.001 TYR C 612 PHE 0.007 0.001 PHE D 235 TRP 0.002 0.000 TRP B 662 HIS 0.003 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00162 (22104) covalent geometry : angle 0.44446 (29940) hydrogen bonds : bond 0.15394 ( 884) hydrogen bonds : angle 5.75975 ( 2616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 0.933 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: symmetry clash REVERT: A 255 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8195 (mt-10) REVERT: A 593 LEU cc_start: 0.9014 (tp) cc_final: 0.8692 (mt) REVERT: A 666 PHE cc_start: 0.8136 (m-80) cc_final: 0.7720 (m-80) REVERT: A 718 ASP cc_start: 0.8287 (t0) cc_final: 0.7926 (m-30) REVERT: B 255 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8215 (mt-10) REVERT: B 433 ASN cc_start: 0.7956 (m110) cc_final: 0.7627 (m-40) REVERT: B 593 LEU cc_start: 0.9027 (tp) cc_final: 0.8686 (mt) REVERT: B 666 PHE cc_start: 0.8177 (m-80) cc_final: 0.7796 (m-80) REVERT: B 700 VAL cc_start: 0.7947 (OUTLIER) cc_final: 0.7746 (m) REVERT: B 718 ASP cc_start: 0.8275 (t0) cc_final: 0.7968 (m-30) REVERT: C 255 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8211 (mt-10) REVERT: C 593 LEU cc_start: 0.9063 (tp) cc_final: 0.8707 (mt) REVERT: C 666 PHE cc_start: 0.8114 (m-80) cc_final: 0.7717 (m-80) REVERT: C 672 LYS cc_start: 0.7564 (ptmt) cc_final: 0.7319 (ttpt) REVERT: C 718 ASP cc_start: 0.8260 (t0) cc_final: 0.7956 (m-30) REVERT: D 255 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8212 (mt-10) REVERT: D 433 ASN cc_start: 0.7873 (m110) cc_final: 0.7600 (m-40) REVERT: D 593 LEU cc_start: 0.9083 (tp) cc_final: 0.8724 (mt) REVERT: D 666 PHE cc_start: 0.8168 (m-80) cc_final: 0.7753 (m-80) REVERT: D 672 LYS cc_start: 0.7508 (ptmt) cc_final: 0.7289 (ttpt) outliers start: 64 outliers final: 18 residues processed: 338 average time/residue: 0.1768 time to fit residues: 90.5087 Evaluate side-chains 184 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 478 VAL Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 700 VAL Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 478 VAL Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 654 LYS Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 GLN A 344 ASN A 617 ASN A 648 GLN A 650 HIS A 656 GLN A 713 GLN A 742 HIS ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 344 ASN B 617 ASN B 648 GLN B 650 HIS B 656 GLN B 713 GLN B 742 HIS ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 310 GLN C 344 ASN C 617 ASN C 648 GLN C 650 HIS C 656 GLN C 713 GLN C 742 HIS D 113 HIS ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 344 ASN D 617 ASN D 648 GLN D 650 HIS D 656 GLN D 713 GLN D 742 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.124820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.075132 restraints weight = 51486.240| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.48 r_work: 0.3062 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22104 Z= 0.161 Angle : 0.582 8.917 29940 Z= 0.303 Chirality : 0.043 0.147 3388 Planarity : 0.003 0.026 3828 Dihedral : 4.536 42.273 2933 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 2.00 % Allowed : 8.94 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.17), residues: 2692 helix: 3.69 (0.17), residues: 748 sheet: -0.94 (0.22), residues: 684 loop : -1.99 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.009 0.001 TYR A 304 PHE 0.020 0.002 PHE D 727 TRP 0.015 0.002 TRP C 733 HIS 0.008 0.002 HIS A 742 Details of bonding type rmsd covalent geometry : bond 0.00369 (22104) covalent geometry : angle 0.58175 (29940) hydrogen bonds : bond 0.03831 ( 884) hydrogen bonds : angle 4.33701 ( 2616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 154 time to evaluate : 0.892 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 255 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8348 (mt-10) REVERT: A 263 LYS cc_start: 0.7531 (pttp) cc_final: 0.7242 (pttt) REVERT: A 402 CYS cc_start: 0.8664 (m) cc_final: 0.7784 (t) REVERT: A 593 LEU cc_start: 0.9079 (tp) cc_final: 0.8638 (mt) REVERT: A 718 ASP cc_start: 0.8289 (t0) cc_final: 0.7939 (m-30) REVERT: A 733 TRP cc_start: 0.8523 (m100) cc_final: 0.8075 (m100) REVERT: B 113 HIS cc_start: 0.8967 (t70) cc_final: 0.8749 (m-70) REVERT: B 255 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 402 CYS cc_start: 0.8493 (m) cc_final: 0.7702 (t) REVERT: B 593 LEU cc_start: 0.9127 (tp) cc_final: 0.8681 (mt) REVERT: B 612 TYR cc_start: 0.8232 (m-80) cc_final: 0.7873 (m-80) REVERT: B 666 PHE cc_start: 0.8368 (m-80) cc_final: 0.8031 (m-80) REVERT: B 672 LYS cc_start: 0.7592 (ptmt) cc_final: 0.7342 (ttpt) REVERT: B 718 ASP cc_start: 0.8333 (t0) cc_final: 0.7962 (m-30) REVERT: B 733 TRP cc_start: 0.8696 (m100) cc_final: 0.8257 (m100) REVERT: C 105 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8921 (tp) REVERT: C 113 HIS cc_start: 0.9004 (t70) cc_final: 0.8745 (m-70) REVERT: C 255 GLU cc_start: 0.8835 (mm-30) cc_final: 0.8360 (mt-10) REVERT: C 402 CYS cc_start: 0.8613 (m) cc_final: 0.7715 (t) REVERT: C 593 LEU cc_start: 0.9147 (tp) cc_final: 0.8687 (mt) REVERT: C 612 TYR cc_start: 0.8258 (m-80) cc_final: 0.7875 (m-80) REVERT: C 666 PHE cc_start: 0.8398 (m-80) cc_final: 0.8001 (m-80) REVERT: C 718 ASP cc_start: 0.8296 (t0) cc_final: 0.7971 (m-30) REVERT: C 733 TRP cc_start: 0.8663 (m100) cc_final: 0.8235 (m100) REVERT: D 255 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8566 (mm-30) REVERT: D 402 CYS cc_start: 0.8725 (m) cc_final: 0.7868 (t) REVERT: D 593 LEU cc_start: 0.9140 (tp) cc_final: 0.8676 (mt) REVERT: D 612 TYR cc_start: 0.8257 (m-80) cc_final: 0.7903 (m-80) REVERT: D 666 PHE cc_start: 0.8402 (m-80) cc_final: 0.8011 (m-80) REVERT: D 733 TRP cc_start: 0.8714 (m100) cc_final: 0.8269 (m100) outliers start: 49 outliers final: 26 residues processed: 190 average time/residue: 0.1519 time to fit residues: 45.9876 Evaluate side-chains 159 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 207 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 75 optimal weight: 0.2980 chunk 265 optimal weight: 7.9990 chunk 162 optimal weight: 5.9990 chunk 106 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 724 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 724 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 GLN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 724 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 GLN ** D 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.125099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.075400 restraints weight = 51850.866| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.47 r_work: 0.3069 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22104 Z= 0.121 Angle : 0.511 6.456 29940 Z= 0.266 Chirality : 0.041 0.140 3388 Planarity : 0.003 0.026 3828 Dihedral : 4.394 42.628 2916 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.21 % Favored : 91.64 % Rotamer: Outliers : 2.08 % Allowed : 9.27 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.17), residues: 2692 helix: 3.62 (0.17), residues: 748 sheet: -1.01 (0.21), residues: 712 loop : -2.00 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 367 TYR 0.010 0.001 TYR B 612 PHE 0.014 0.001 PHE D 727 TRP 0.010 0.001 TRP C 733 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00275 (22104) covalent geometry : angle 0.51105 (29940) hydrogen bonds : bond 0.03540 ( 884) hydrogen bonds : angle 4.07872 ( 2616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8363 (mt-10) REVERT: A 263 LYS cc_start: 0.7559 (pttp) cc_final: 0.7276 (pttt) REVERT: A 402 CYS cc_start: 0.8472 (m) cc_final: 0.7744 (t) REVERT: A 593 LEU cc_start: 0.9099 (tp) cc_final: 0.8652 (mt) REVERT: A 612 TYR cc_start: 0.8249 (m-80) cc_final: 0.7808 (m-80) REVERT: A 717 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7004 (mt) REVERT: A 718 ASP cc_start: 0.8308 (t0) cc_final: 0.7955 (m-30) REVERT: A 733 TRP cc_start: 0.8732 (m100) cc_final: 0.8152 (m100) REVERT: A 792 MET cc_start: 0.8747 (ppp) cc_final: 0.7939 (ppp) REVERT: B 255 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8366 (mt-10) REVERT: B 402 CYS cc_start: 0.8476 (m) cc_final: 0.7748 (t) REVERT: B 432 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8726 (mt) REVERT: B 593 LEU cc_start: 0.9146 (tp) cc_final: 0.8719 (mt) REVERT: B 612 TYR cc_start: 0.8246 (m-80) cc_final: 0.7811 (m-80) REVERT: B 666 PHE cc_start: 0.8380 (m-80) cc_final: 0.8014 (m-80) REVERT: B 792 MET cc_start: 0.8660 (ppp) cc_final: 0.7848 (ppp) REVERT: C 255 GLU cc_start: 0.8793 (mm-30) cc_final: 0.8393 (mt-10) REVERT: C 402 CYS cc_start: 0.8496 (m) cc_final: 0.7776 (t) REVERT: C 432 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8726 (mt) REVERT: C 593 LEU cc_start: 0.9153 (tp) cc_final: 0.8719 (mt) REVERT: C 612 TYR cc_start: 0.8275 (m-80) cc_final: 0.7823 (m-80) REVERT: C 666 PHE cc_start: 0.8374 (m-80) cc_final: 0.7999 (m-80) REVERT: C 717 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7178 (mt) REVERT: C 718 ASP cc_start: 0.8360 (t0) cc_final: 0.7969 (m-30) REVERT: C 733 TRP cc_start: 0.8825 (m100) cc_final: 0.8241 (m100) REVERT: C 792 MET cc_start: 0.8738 (ppp) cc_final: 0.7812 (ppp) REVERT: D 255 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8406 (mt-10) REVERT: D 402 CYS cc_start: 0.8526 (m) cc_final: 0.7795 (t) REVERT: D 432 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8702 (mt) REVERT: D 593 LEU cc_start: 0.9160 (tp) cc_final: 0.8694 (mt) REVERT: D 612 TYR cc_start: 0.8171 (m-80) cc_final: 0.7741 (m-80) REVERT: D 666 PHE cc_start: 0.8397 (m-80) cc_final: 0.8027 (m-80) REVERT: D 717 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6662 (mt) REVERT: D 733 TRP cc_start: 0.8812 (m100) cc_final: 0.8204 (m100) REVERT: D 765 THR cc_start: 0.7721 (t) cc_final: 0.7498 (m) REVERT: D 792 MET cc_start: 0.8780 (ppp) cc_final: 0.7763 (ppp) outliers start: 51 outliers final: 27 residues processed: 195 average time/residue: 0.1449 time to fit residues: 46.0368 Evaluate side-chains 165 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 209 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 94 optimal weight: 0.8980 chunk 175 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 188 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 117 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 224 optimal weight: 0.0010 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 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 = 0.4189 r_free = 0.4189 target = 0.124969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.074313 restraints weight = 51699.187| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.48 r_work: 0.3039 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22104 Z= 0.139 Angle : 0.528 8.977 29940 Z= 0.273 Chirality : 0.042 0.143 3388 Planarity : 0.003 0.028 3828 Dihedral : 4.479 43.294 2916 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.62 % Favored : 91.23 % Rotamer: Outliers : 1.71 % Allowed : 10.65 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2692 helix: 3.55 (0.17), residues: 748 sheet: -0.94 (0.21), residues: 712 loop : -2.04 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 367 TYR 0.010 0.001 TYR D 479 PHE 0.013 0.001 PHE C 235 TRP 0.008 0.001 TRP B 733 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00320 (22104) covalent geometry : angle 0.52841 (29940) hydrogen bonds : bond 0.03667 ( 884) hydrogen bonds : angle 4.05146 ( 2616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8373 (mt-10) REVERT: A 263 LYS cc_start: 0.7617 (pttp) cc_final: 0.7326 (pttt) REVERT: A 549 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7829 (mp0) REVERT: A 593 LEU cc_start: 0.9111 (tp) cc_final: 0.8672 (mt) REVERT: A 612 TYR cc_start: 0.8302 (m-80) cc_final: 0.7841 (m-80) REVERT: A 717 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7165 (mt) REVERT: A 718 ASP cc_start: 0.8307 (t0) cc_final: 0.8007 (m-30) REVERT: A 792 MET cc_start: 0.8735 (ppp) cc_final: 0.7842 (ppp) REVERT: B 255 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8382 (mt-10) REVERT: B 402 CYS cc_start: 0.8508 (m) cc_final: 0.7792 (t) REVERT: B 549 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7864 (mp0) REVERT: B 593 LEU cc_start: 0.9180 (tp) cc_final: 0.8744 (mt) REVERT: B 612 TYR cc_start: 0.8219 (m-80) cc_final: 0.7813 (m-80) REVERT: B 666 PHE cc_start: 0.8374 (m-80) cc_final: 0.8006 (m-80) REVERT: B 717 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6344 (pt) REVERT: C 255 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8375 (mt-10) REVERT: C 549 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7858 (mp0) REVERT: C 593 LEU cc_start: 0.9167 (tp) cc_final: 0.8721 (mt) REVERT: C 612 TYR cc_start: 0.8318 (m-80) cc_final: 0.7841 (m-80) REVERT: C 666 PHE cc_start: 0.8370 (m-80) cc_final: 0.7983 (m-80) REVERT: C 717 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7115 (mt) REVERT: C 718 ASP cc_start: 0.8318 (t0) cc_final: 0.7972 (m-30) REVERT: D 255 GLU cc_start: 0.8790 (mm-30) cc_final: 0.8383 (mt-10) REVERT: D 593 LEU cc_start: 0.9168 (tp) cc_final: 0.8716 (mt) REVERT: D 612 TYR cc_start: 0.8194 (m-80) cc_final: 0.7790 (m-80) REVERT: D 666 PHE cc_start: 0.8376 (m-80) cc_final: 0.8008 (m-80) REVERT: D 717 LEU cc_start: 0.7127 (OUTLIER) cc_final: 0.6892 (mt) outliers start: 42 outliers final: 28 residues processed: 180 average time/residue: 0.1503 time to fit residues: 44.5518 Evaluate side-chains 163 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 72 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 76 optimal weight: 0.0980 chunk 135 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 201 optimal weight: 0.6980 chunk 255 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 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 = 0.4186 r_free = 0.4186 target = 0.124297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074373 restraints weight = 51048.234| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 3.43 r_work: 0.3041 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22104 Z= 0.130 Angle : 0.512 8.008 29940 Z= 0.266 Chirality : 0.041 0.141 3388 Planarity : 0.003 0.027 3828 Dihedral : 4.485 43.816 2916 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.32 % Favored : 91.53 % Rotamer: Outliers : 1.67 % Allowed : 11.59 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2692 helix: 3.56 (0.17), residues: 748 sheet: -0.94 (0.21), residues: 712 loop : -2.05 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.011 0.001 TYR A 479 PHE 0.011 0.001 PHE D 319 TRP 0.010 0.001 TRP A 733 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00300 (22104) covalent geometry : angle 0.51213 (29940) hydrogen bonds : bond 0.03593 ( 884) hydrogen bonds : angle 4.00253 ( 2616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 140 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8371 (mt-10) REVERT: A 263 LYS cc_start: 0.7517 (pttp) cc_final: 0.7231 (pttt) REVERT: A 402 CYS cc_start: 0.8404 (m) cc_final: 0.7565 (t) REVERT: A 549 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7839 (mp0) REVERT: A 593 LEU cc_start: 0.9121 (tp) cc_final: 0.8668 (mt) REVERT: A 612 TYR cc_start: 0.8309 (m-80) cc_final: 0.7821 (m-80) REVERT: B 255 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8383 (mt-10) REVERT: B 432 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 433 ASN cc_start: 0.8323 (m110) cc_final: 0.7663 (m110) REVERT: B 549 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7876 (mp0) REVERT: B 593 LEU cc_start: 0.9179 (tp) cc_final: 0.8740 (mt) REVERT: B 612 TYR cc_start: 0.8257 (m-80) cc_final: 0.7871 (m-80) REVERT: B 666 PHE cc_start: 0.8350 (m-80) cc_final: 0.7999 (m-80) REVERT: C 255 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8370 (mt-10) REVERT: C 402 CYS cc_start: 0.8474 (m) cc_final: 0.7669 (t) REVERT: C 549 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7772 (mp0) REVERT: C 593 LEU cc_start: 0.9169 (tp) cc_final: 0.8717 (mt) REVERT: C 612 TYR cc_start: 0.8324 (m-80) cc_final: 0.7830 (m-80) REVERT: C 666 PHE cc_start: 0.8373 (m-80) cc_final: 0.7984 (m-80) REVERT: C 717 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7433 (mt) REVERT: D 255 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8381 (mt-10) REVERT: D 402 CYS cc_start: 0.8513 (m) cc_final: 0.7677 (t) REVERT: D 432 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8488 (mp) REVERT: D 549 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7800 (mp0) REVERT: D 593 LEU cc_start: 0.9172 (tp) cc_final: 0.8716 (mt) REVERT: D 612 TYR cc_start: 0.8230 (m-80) cc_final: 0.7847 (m-80) REVERT: D 666 PHE cc_start: 0.8382 (m-80) cc_final: 0.8008 (m-80) REVERT: D 717 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6900 (pt) outliers start: 41 outliers final: 27 residues processed: 172 average time/residue: 0.1432 time to fit residues: 40.0887 Evaluate side-chains 160 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 432 LEU Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 35 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 180 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 124 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 144 optimal weight: 0.4980 chunk 115 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 596 ASN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 596 ASN ** D 648 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 = 0.4176 r_free = 0.4176 target = 0.123796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.073454 restraints weight = 51411.772| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.46 r_work: 0.3033 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22104 Z= 0.143 Angle : 0.519 7.234 29940 Z= 0.271 Chirality : 0.041 0.143 3388 Planarity : 0.003 0.028 3828 Dihedral : 4.521 44.340 2916 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.32 % Favored : 91.53 % Rotamer: Outliers : 1.80 % Allowed : 12.29 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2692 helix: 3.54 (0.17), residues: 744 sheet: -1.04 (0.20), residues: 724 loop : -2.03 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 367 TYR 0.009 0.001 TYR D 479 PHE 0.017 0.001 PHE C 796 TRP 0.012 0.001 TRP A 733 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00333 (22104) covalent geometry : angle 0.51900 (29940) hydrogen bonds : bond 0.03762 ( 884) hydrogen bonds : angle 4.03137 ( 2616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8378 (mt-10) REVERT: A 263 LYS cc_start: 0.7595 (pttp) cc_final: 0.7275 (pttt) REVERT: A 402 CYS cc_start: 0.8427 (m) cc_final: 0.7615 (t) REVERT: A 549 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7818 (mp0) REVERT: A 593 LEU cc_start: 0.9141 (tp) cc_final: 0.8682 (mt) REVERT: A 612 TYR cc_start: 0.8310 (m-80) cc_final: 0.7809 (m-80) REVERT: B 255 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8465 (mm-30) REVERT: B 402 CYS cc_start: 0.8430 (m) cc_final: 0.7528 (t) REVERT: B 549 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7878 (mp0) REVERT: B 593 LEU cc_start: 0.9222 (tp) cc_final: 0.8771 (mt) REVERT: B 612 TYR cc_start: 0.8249 (m-80) cc_final: 0.7883 (m-80) REVERT: B 666 PHE cc_start: 0.8377 (m-80) cc_final: 0.7998 (m-80) REVERT: B 717 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6566 (pt) REVERT: C 255 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8377 (mt-10) REVERT: C 263 LYS cc_start: 0.7622 (pttp) cc_final: 0.7319 (pttt) REVERT: C 402 CYS cc_start: 0.8483 (m) cc_final: 0.7652 (t) REVERT: C 433 ASN cc_start: 0.8272 (m110) cc_final: 0.7864 (m110) REVERT: C 549 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7834 (mp0) REVERT: C 593 LEU cc_start: 0.9226 (tp) cc_final: 0.8773 (mt) REVERT: C 612 TYR cc_start: 0.8336 (m-80) cc_final: 0.7822 (m-80) REVERT: C 666 PHE cc_start: 0.8361 (m-80) cc_final: 0.7990 (m-80) REVERT: D 255 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8475 (mm-30) REVERT: D 402 CYS cc_start: 0.8578 (m) cc_final: 0.7728 (t) REVERT: D 549 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7861 (mp0) REVERT: D 593 LEU cc_start: 0.9227 (tp) cc_final: 0.8767 (mt) REVERT: D 612 TYR cc_start: 0.8256 (m-80) cc_final: 0.7882 (m-80) REVERT: D 666 PHE cc_start: 0.8387 (m-80) cc_final: 0.8013 (m-80) REVERT: D 717 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6916 (pt) outliers start: 44 outliers final: 29 residues processed: 172 average time/residue: 0.1358 time to fit residues: 38.6453 Evaluate side-chains 158 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 155 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 112 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 224 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 123 optimal weight: 0.0970 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 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 = 0.4179 r_free = 0.4179 target = 0.124025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.073391 restraints weight = 51323.547| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.44 r_work: 0.3034 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22104 Z= 0.143 Angle : 0.520 6.734 29940 Z= 0.271 Chirality : 0.041 0.142 3388 Planarity : 0.003 0.031 3828 Dihedral : 4.540 44.856 2916 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.25 % Favored : 91.64 % Rotamer: Outliers : 1.76 % Allowed : 12.90 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.17), residues: 2692 helix: 3.51 (0.17), residues: 744 sheet: -1.10 (0.20), residues: 732 loop : -2.00 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 367 TYR 0.009 0.001 TYR C 723 PHE 0.013 0.001 PHE C 235 TRP 0.014 0.001 TRP B 733 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00332 (22104) covalent geometry : angle 0.52010 (29940) hydrogen bonds : bond 0.03733 ( 884) hydrogen bonds : angle 4.01373 ( 2616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8480 (mm-30) REVERT: A 263 LYS cc_start: 0.7637 (pttp) cc_final: 0.7347 (pttt) REVERT: A 402 CYS cc_start: 0.8406 (m) cc_final: 0.7619 (t) REVERT: A 549 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7772 (mp0) REVERT: A 593 LEU cc_start: 0.9184 (tp) cc_final: 0.8707 (mt) REVERT: A 612 TYR cc_start: 0.8301 (m-80) cc_final: 0.7792 (m-80) REVERT: A 717 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6265 (pt) REVERT: B 255 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8476 (mm-30) REVERT: B 402 CYS cc_start: 0.8427 (m) cc_final: 0.7595 (t) REVERT: B 593 LEU cc_start: 0.9231 (tp) cc_final: 0.8755 (mt) REVERT: B 612 TYR cc_start: 0.8267 (m-80) cc_final: 0.7915 (m-80) REVERT: B 636 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8991 (mp) REVERT: B 666 PHE cc_start: 0.8399 (m-80) cc_final: 0.8026 (m-80) REVERT: B 717 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6533 (pt) REVERT: C 255 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8470 (mm-30) REVERT: C 263 LYS cc_start: 0.7625 (pttp) cc_final: 0.7335 (pttt) REVERT: C 402 CYS cc_start: 0.8495 (m) cc_final: 0.7732 (t) REVERT: C 549 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7799 (mp0) REVERT: C 593 LEU cc_start: 0.9234 (tp) cc_final: 0.8780 (mt) REVERT: C 612 TYR cc_start: 0.8360 (m-80) cc_final: 0.7833 (m-80) REVERT: C 666 PHE cc_start: 0.8394 (m-80) cc_final: 0.8022 (m-80) REVERT: D 255 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8477 (mm-30) REVERT: D 263 LYS cc_start: 0.7633 (pttp) cc_final: 0.7335 (pttt) REVERT: D 387 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8277 (pp30) REVERT: D 402 CYS cc_start: 0.8499 (m) cc_final: 0.7699 (t) REVERT: D 549 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7854 (mp0) REVERT: D 593 LEU cc_start: 0.9229 (tp) cc_final: 0.8773 (mt) REVERT: D 612 TYR cc_start: 0.8261 (m-80) cc_final: 0.7902 (m-80) REVERT: D 666 PHE cc_start: 0.8407 (m-80) cc_final: 0.8042 (m-80) outliers start: 43 outliers final: 31 residues processed: 164 average time/residue: 0.1439 time to fit residues: 39.3070 Evaluate side-chains 161 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 480 MET Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 138 optimal weight: 0.6980 chunk 266 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 234 optimal weight: 4.9990 chunk 163 optimal weight: 0.9990 chunk 34 optimal weight: 0.0970 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 ASN ** D 648 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 = 0.4176 r_free = 0.4176 target = 0.123858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.073657 restraints weight = 51185.505| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.40 r_work: 0.3024 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22104 Z= 0.141 Angle : 0.527 10.734 29940 Z= 0.275 Chirality : 0.041 0.141 3388 Planarity : 0.003 0.031 3828 Dihedral : 4.548 44.720 2916 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.14 % Favored : 91.75 % Rotamer: Outliers : 1.76 % Allowed : 13.02 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.17), residues: 2692 helix: 3.49 (0.17), residues: 744 sheet: -1.07 (0.20), residues: 732 loop : -1.99 (0.17), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.009 0.001 TYR D 411 PHE 0.012 0.001 PHE C 235 TRP 0.015 0.001 TRP A 733 HIS 0.003 0.001 HIS B 650 Details of bonding type rmsd covalent geometry : bond 0.00328 (22104) covalent geometry : angle 0.52669 (29940) hydrogen bonds : bond 0.03728 ( 884) hydrogen bonds : angle 3.98980 ( 2616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8469 (mm-30) REVERT: A 263 LYS cc_start: 0.7635 (pttp) cc_final: 0.7332 (pttt) REVERT: A 402 CYS cc_start: 0.8365 (m) cc_final: 0.7556 (t) REVERT: A 593 LEU cc_start: 0.9187 (tp) cc_final: 0.8708 (mt) REVERT: A 612 TYR cc_start: 0.8334 (m-80) cc_final: 0.7827 (m-80) REVERT: A 717 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6199 (pt) REVERT: B 255 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8467 (mm-30) REVERT: B 263 LYS cc_start: 0.7642 (pttp) cc_final: 0.7340 (pttt) REVERT: B 402 CYS cc_start: 0.8408 (m) cc_final: 0.7539 (t) REVERT: B 593 LEU cc_start: 0.9243 (tp) cc_final: 0.8767 (mt) REVERT: B 612 TYR cc_start: 0.8270 (m-80) cc_final: 0.7933 (m-80) REVERT: B 636 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8857 (mp) REVERT: B 666 PHE cc_start: 0.8361 (m-80) cc_final: 0.7999 (m-80) REVERT: C 255 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8459 (mm-30) REVERT: C 263 LYS cc_start: 0.7651 (pttp) cc_final: 0.7349 (pttt) REVERT: C 402 CYS cc_start: 0.8478 (m) cc_final: 0.7645 (t) REVERT: C 549 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7830 (mp0) REVERT: C 593 LEU cc_start: 0.9236 (tp) cc_final: 0.8778 (mt) REVERT: C 612 TYR cc_start: 0.8362 (m-80) cc_final: 0.7851 (m-80) REVERT: C 636 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8830 (mp) REVERT: C 666 PHE cc_start: 0.8398 (m-80) cc_final: 0.7997 (m-80) REVERT: D 255 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 263 LYS cc_start: 0.7642 (pttp) cc_final: 0.7335 (pttt) REVERT: D 387 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8282 (pp30) REVERT: D 402 CYS cc_start: 0.8507 (m) cc_final: 0.7679 (t) REVERT: D 549 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7872 (mp0) REVERT: D 593 LEU cc_start: 0.9234 (tp) cc_final: 0.8774 (mt) REVERT: D 612 TYR cc_start: 0.8272 (m-80) cc_final: 0.7924 (m-80) REVERT: D 636 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8865 (mp) REVERT: D 666 PHE cc_start: 0.8395 (m-80) cc_final: 0.8033 (m-80) REVERT: D 717 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7017 (pt) outliers start: 43 outliers final: 32 residues processed: 162 average time/residue: 0.1411 time to fit residues: 37.9600 Evaluate side-chains 167 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 129 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 391 GLU Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 33 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 63 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 193 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 262 optimal weight: 0.4980 chunk 188 optimal weight: 7.9990 chunk 134 optimal weight: 0.0040 chunk 94 optimal weight: 0.8980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 639 ASN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 639 ASN ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 639 ASN ** D 648 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 = 0.4185 r_free = 0.4185 target = 0.124460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.074397 restraints weight = 51316.844| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 3.46 r_work: 0.3052 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22104 Z= 0.120 Angle : 0.519 11.092 29940 Z= 0.269 Chirality : 0.041 0.199 3388 Planarity : 0.003 0.030 3828 Dihedral : 4.524 45.380 2916 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 1.55 % Allowed : 13.35 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2692 helix: 3.51 (0.17), residues: 748 sheet: -0.93 (0.21), residues: 708 loop : -2.00 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 367 TYR 0.010 0.001 TYR A 411 PHE 0.011 0.001 PHE C 235 TRP 0.017 0.001 TRP A 733 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00276 (22104) covalent geometry : angle 0.51914 (29940) hydrogen bonds : bond 0.03483 ( 884) hydrogen bonds : angle 3.87892 ( 2616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8372 (mt-10) REVERT: A 263 LYS cc_start: 0.7697 (pttp) cc_final: 0.7382 (pttt) REVERT: A 402 CYS cc_start: 0.8405 (m) cc_final: 0.7588 (t) REVERT: A 433 ASN cc_start: 0.8236 (m110) cc_final: 0.7659 (m-40) REVERT: A 466 ASP cc_start: 0.7897 (t0) cc_final: 0.6822 (p0) REVERT: A 549 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7755 (mp0) REVERT: A 593 LEU cc_start: 0.9199 (tp) cc_final: 0.8730 (mt) REVERT: A 612 TYR cc_start: 0.8352 (m-80) cc_final: 0.7851 (m-80) REVERT: A 622 MET cc_start: 0.7416 (OUTLIER) cc_final: 0.7057 (mtm) REVERT: B 255 GLU cc_start: 0.8750 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 263 LYS cc_start: 0.7707 (pttp) cc_final: 0.7389 (pttt) REVERT: B 402 CYS cc_start: 0.8395 (m) cc_final: 0.7537 (t) REVERT: B 593 LEU cc_start: 0.9234 (tp) cc_final: 0.8757 (mt) REVERT: B 612 TYR cc_start: 0.8299 (m-80) cc_final: 0.7973 (m-80) REVERT: B 636 ILE cc_start: 0.9029 (OUTLIER) cc_final: 0.8814 (mp) REVERT: B 666 PHE cc_start: 0.8381 (m-80) cc_final: 0.8036 (m-80) REVERT: C 255 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8365 (mt-10) REVERT: C 263 LYS cc_start: 0.7709 (pttp) cc_final: 0.7397 (pttt) REVERT: C 402 CYS cc_start: 0.8494 (m) cc_final: 0.7668 (t) REVERT: C 549 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7799 (mp0) REVERT: C 593 LEU cc_start: 0.9225 (tp) cc_final: 0.8771 (mt) REVERT: C 612 TYR cc_start: 0.8367 (m-80) cc_final: 0.7851 (m-80) REVERT: C 636 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8825 (mp) REVERT: C 666 PHE cc_start: 0.8409 (m-80) cc_final: 0.8017 (m-80) REVERT: D 255 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8367 (mt-10) REVERT: D 263 LYS cc_start: 0.7711 (pttp) cc_final: 0.7389 (pttt) REVERT: D 387 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8274 (pp30) REVERT: D 402 CYS cc_start: 0.8504 (m) cc_final: 0.7674 (t) REVERT: D 549 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7868 (mp0) REVERT: D 593 LEU cc_start: 0.9229 (tp) cc_final: 0.8767 (mt) REVERT: D 612 TYR cc_start: 0.8308 (m-80) cc_final: 0.7970 (m-80) REVERT: D 636 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8781 (mp) REVERT: D 666 PHE cc_start: 0.8398 (m-80) cc_final: 0.8058 (m-80) REVERT: D 717 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6980 (pt) outliers start: 38 outliers final: 30 residues processed: 164 average time/residue: 0.1368 time to fit residues: 37.2491 Evaluate side-chains 169 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 65 optimal weight: 7.9990 chunk 202 optimal weight: 3.9990 chunk 90 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 42 optimal weight: 0.3980 chunk 199 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 235 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 GLN D 648 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.123989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.073796 restraints weight = 51423.948| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.46 r_work: 0.3041 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22104 Z= 0.130 Angle : 0.534 10.367 29940 Z= 0.276 Chirality : 0.042 0.204 3388 Planarity : 0.003 0.030 3828 Dihedral : 4.517 45.521 2916 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 1.71 % Allowed : 13.67 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.17), residues: 2692 helix: 3.47 (0.17), residues: 748 sheet: -0.97 (0.20), residues: 740 loop : -2.05 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 367 TYR 0.010 0.001 TYR A 411 PHE 0.012 0.001 PHE C 235 TRP 0.017 0.001 TRP A 733 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00303 (22104) covalent geometry : angle 0.53416 (29940) hydrogen bonds : bond 0.03613 ( 884) hydrogen bonds : angle 3.87752 ( 2616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5384 Ramachandran restraints generated. 2692 Oldfield, 0 Emsley, 2692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8345 (mt-10) REVERT: A 263 LYS cc_start: 0.7716 (pttp) cc_final: 0.7401 (pttt) REVERT: A 402 CYS cc_start: 0.8414 (m) cc_final: 0.7593 (t) REVERT: A 433 ASN cc_start: 0.8254 (m110) cc_final: 0.7725 (m110) REVERT: A 466 ASP cc_start: 0.7948 (t0) cc_final: 0.6902 (p0) REVERT: A 549 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7769 (mp0) REVERT: A 593 LEU cc_start: 0.9203 (tp) cc_final: 0.8735 (mt) REVERT: A 612 TYR cc_start: 0.8355 (m-80) cc_final: 0.7862 (m-80) REVERT: A 622 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7089 (mtm) REVERT: B 255 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8456 (mm-30) REVERT: B 263 LYS cc_start: 0.7741 (pttp) cc_final: 0.7426 (pttt) REVERT: B 402 CYS cc_start: 0.8390 (m) cc_final: 0.7526 (t) REVERT: B 593 LEU cc_start: 0.9245 (tp) cc_final: 0.8771 (mt) REVERT: B 612 TYR cc_start: 0.8251 (m-80) cc_final: 0.7930 (m-80) REVERT: B 636 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8831 (mp) REVERT: B 666 PHE cc_start: 0.8425 (m-80) cc_final: 0.8076 (m-80) REVERT: C 255 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8348 (mt-10) REVERT: C 263 LYS cc_start: 0.7743 (pttp) cc_final: 0.7436 (pttt) REVERT: C 402 CYS cc_start: 0.8505 (m) cc_final: 0.7674 (t) REVERT: C 549 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7818 (mp0) REVERT: C 593 LEU cc_start: 0.9231 (tp) cc_final: 0.8776 (mt) REVERT: C 612 TYR cc_start: 0.8360 (m-80) cc_final: 0.7852 (m-80) REVERT: C 636 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8723 (mp) REVERT: C 666 PHE cc_start: 0.8413 (m-80) cc_final: 0.8020 (m-80) REVERT: D 255 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8357 (mt-10) REVERT: D 263 LYS cc_start: 0.7741 (pttp) cc_final: 0.7425 (pttt) REVERT: D 387 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8274 (pp30) REVERT: D 402 CYS cc_start: 0.8499 (m) cc_final: 0.7689 (t) REVERT: D 549 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7876 (mp0) REVERT: D 593 LEU cc_start: 0.9232 (tp) cc_final: 0.8776 (mt) REVERT: D 612 TYR cc_start: 0.8291 (m-80) cc_final: 0.7961 (m-80) REVERT: D 636 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8744 (mp) REVERT: D 666 PHE cc_start: 0.8396 (m-80) cc_final: 0.8040 (m-80) REVERT: D 717 LEU cc_start: 0.7291 (OUTLIER) cc_final: 0.6936 (pt) outliers start: 42 outliers final: 33 residues processed: 167 average time/residue: 0.1385 time to fit residues: 37.9344 Evaluate side-chains 174 residues out of total 2460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 135 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 480 MET Chi-restraints excluded: chain A residue 622 MET Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 729 PHE Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 769 LYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 397 ILE Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain B residue 622 MET Chi-restraints excluded: chain B residue 636 ILE Chi-restraints excluded: chain B residue 696 ILE Chi-restraints excluded: chain B residue 729 PHE Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 769 LYS Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 397 ILE Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 636 ILE Chi-restraints excluded: chain C residue 696 ILE Chi-restraints excluded: chain C residue 729 PHE Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 769 LYS Chi-restraints excluded: chain D residue 211 THR Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 391 GLU Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 432 LEU Chi-restraints excluded: chain D residue 622 MET Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 696 ILE Chi-restraints excluded: chain D residue 717 LEU Chi-restraints excluded: chain D residue 729 PHE Chi-restraints excluded: chain D residue 736 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 225 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 192 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 75 optimal weight: 0.0270 chunk 9 optimal weight: 0.7980 chunk 32 optimal weight: 0.0870 chunk 80 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 172 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN ** A 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 GLN B 639 ASN B 648 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 GLN C 648 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 ASN ** 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 = 0.4193 r_free = 0.4193 target = 0.125017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.074890 restraints weight = 51235.369| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.48 r_work: 0.3067 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 22104 Z= 0.106 Angle : 0.516 10.792 29940 Z= 0.266 Chirality : 0.041 0.209 3388 Planarity : 0.003 0.030 3828 Dihedral : 4.488 46.127 2916 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 1.76 % Allowed : 13.63 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.17), residues: 2692 helix: 3.51 (0.17), residues: 752 sheet: -0.85 (0.21), residues: 708 loop : -2.01 (0.17), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 367 TYR 0.009 0.001 TYR A 411 PHE 0.009 0.001 PHE C 319 TRP 0.017 0.001 TRP A 733 HIS 0.003 0.001 HIS D 650 Details of bonding type rmsd covalent geometry : bond 0.00243 (22104) covalent geometry : angle 0.51570 (29940) hydrogen bonds : bond 0.03306 ( 884) hydrogen bonds : angle 3.78594 ( 2616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7360.28 seconds wall clock time: 126 minutes 32.33 seconds (7592.33 seconds total)