Starting phenix.real_space_refine on Sat Oct 11 16:30:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3s_36858/10_2025/8k3s_36858_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3s_36858/10_2025/8k3s_36858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k3s_36858/10_2025/8k3s_36858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3s_36858/10_2025/8k3s_36858.map" model { file = "/net/cci-nas-00/data/ceres_data/8k3s_36858/10_2025/8k3s_36858_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3s_36858/10_2025/8k3s_36858_neut_trim.cif" } resolution = 3.0 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 4 5.49 5 S 80 5.16 5 C 10424 2.51 5 N 2444 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15761 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3856 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 12, 'TRANS': 453} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 85 Unusual residues: {' CA': 1, 'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 15761 At special positions: 0 Unit cell: (107.613, 107.613, 96.743, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 80 16.00 P 4 15.00 O 2808 8.00 N 2444 7.00 C 10424 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS D 331 " - pdb=" SG CYS D 344 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied NAG-ASN " NAG A 802 " - " ASN A 328 " " NAG A 803 " - " ASN A 362 " " NAG A 804 " - " ASN A 375 " " NAG B 802 " - " ASN B 328 " " NAG B 803 " - " ASN B 362 " " NAG B 804 " - " ASN B 375 " " NAG C 802 " - " ASN C 328 " " NAG C 803 " - " ASN C 362 " " NAG C 804 " - " ASN C 375 " " NAG D 802 " - " ASN D 328 " " NAG D 803 " - " ASN D 362 " " NAG D 804 " - " ASN D 375 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 733.6 milliseconds Enol-peptide restraints added in 1.2 microseconds 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 11 sheets defined 54.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'A' and resid 215 through 242 Processing helix chain 'A' and resid 246 through 259 removed outlier: 3.638A pdb=" N THR A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 284 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 398 through 412 Processing helix chain 'A' and resid 467 through 493 removed outlier: 3.613A pdb=" N PHE A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 493 " --> pdb=" O VAL A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 529 removed outlier: 4.050A pdb=" N VAL A 513 " --> pdb=" O CYS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 removed outlier: 3.707A pdb=" N GLN A 537 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE A 538 " --> pdb=" O LEU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 572 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.769A pdb=" N ILE A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 5.908A pdb=" N THR A 582 " --> pdb=" O PHE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 592 removed outlier: 4.518A pdb=" N THR A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 619 Processing helix chain 'A' and resid 629 through 642 removed outlier: 3.509A pdb=" N ILE A 633 " --> pdb=" O PHE A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 653 removed outlier: 3.879A pdb=" N ILE A 649 " --> pdb=" O ASN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 686 removed outlier: 3.635A pdb=" N ILE A 659 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE A 669 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 242 Processing helix chain 'B' and resid 246 through 259 removed outlier: 3.656A pdb=" N THR B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 284 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 398 through 412 Processing helix chain 'B' and resid 467 through 493 removed outlier: 3.635A pdb=" N PHE B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU B 493 " --> pdb=" O VAL B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 529 removed outlier: 4.001A pdb=" N VAL B 513 " --> pdb=" O CYS B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.655A pdb=" N GLN B 537 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N PHE B 538 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 572 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.709A pdb=" N ILE B 577 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 581 No H-bonds generated for 'chain 'B' and resid 579 through 581' Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.944A pdb=" N THR B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 619 Processing helix chain 'B' and resid 629 through 642 Processing helix chain 'B' and resid 645 through 653 removed outlier: 3.872A pdb=" N ILE B 649 " --> pdb=" O ASN B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 686 removed outlier: 3.522A pdb=" N ILE B 659 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE B 669 " --> pdb=" O VAL B 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 242 Processing helix chain 'C' and resid 246 through 259 removed outlier: 3.643A pdb=" N THR C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 308 through 312 Processing helix chain 'C' and resid 398 through 412 Processing helix chain 'C' and resid 467 through 493 removed outlier: 3.563A pdb=" N PHE C 471 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 529 removed outlier: 3.994A pdb=" N VAL C 513 " --> pdb=" O CYS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 540 removed outlier: 3.658A pdb=" N GLN C 537 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N PHE C 538 " --> pdb=" O LEU C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 572 Processing helix chain 'C' and resid 573 through 578 removed outlier: 3.723A pdb=" N ILE C 577 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 581 No H-bonds generated for 'chain 'C' and resid 579 through 581' Processing helix chain 'C' and resid 582 through 593 removed outlier: 4.057A pdb=" N THR C 588 " --> pdb=" O SER C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 595 through 600 removed outlier: 3.533A pdb=" N PHE C 600 " --> pdb=" O ASP C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 619 Processing helix chain 'C' and resid 629 through 642 Processing helix chain 'C' and resid 645 through 653 removed outlier: 3.870A pdb=" N ILE C 649 " --> pdb=" O ASN C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 686 removed outlier: 3.507A pdb=" N ILE C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE C 669 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 242 Processing helix chain 'D' and resid 246 through 259 removed outlier: 3.645A pdb=" N THR D 250 " --> pdb=" O VAL D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 285 through 290 Processing helix chain 'D' and resid 308 through 312 Processing helix chain 'D' and resid 398 through 412 Processing helix chain 'D' and resid 467 through 493 removed outlier: 3.620A pdb=" N PHE D 471 " --> pdb=" O THR D 467 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 493 " --> pdb=" O VAL D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 529 removed outlier: 4.016A pdb=" N VAL D 513 " --> pdb=" O CYS D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 540 removed outlier: 3.711A pdb=" N GLN D 537 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE D 538 " --> pdb=" O LEU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 572 Processing helix chain 'D' and resid 573 through 578 removed outlier: 3.725A pdb=" N ILE D 577 " --> pdb=" O LEU D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 581 No H-bonds generated for 'chain 'D' and resid 579 through 581' Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.538A pdb=" N LEU D 586 " --> pdb=" O THR D 582 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR D 588 " --> pdb=" O SER D 584 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR D 589 " --> pdb=" O GLN D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 595 through 600 removed outlier: 3.502A pdb=" N GLY D 599 " --> pdb=" O LYS D 595 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE D 600 " --> pdb=" O ASP D 596 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 595 through 600' Processing helix chain 'D' and resid 601 through 619 Processing helix chain 'D' and resid 629 through 642 Processing helix chain 'D' and resid 645 through 653 removed outlier: 3.894A pdb=" N ILE D 649 " --> pdb=" O ASN D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 686 removed outlier: 3.753A pdb=" N PHE D 669 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.170A pdb=" N LEU A 316 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL A 428 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 8.830A pdb=" N VAL A 318 " --> pdb=" O PHE A 426 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N PHE A 426 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG A 320 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE A 424 " --> pdb=" O ARG A 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG A 322 " --> pdb=" O THR A 422 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR A 422 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N LEU A 324 " --> pdb=" O ARG A 420 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 435 " --> pdb=" O ASN A 430 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA3, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.129A pdb=" N LEU B 316 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 428 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL B 318 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 426 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 391 through 394 removed outlier: 6.129A pdb=" N LEU B 316 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL B 428 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 8.813A pdb=" N VAL B 318 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 426 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG B 320 " --> pdb=" O ILE B 424 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE B 424 " --> pdb=" O ARG B 320 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG B 322 " --> pdb=" O THR B 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR B 422 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 324 " --> pdb=" O ARG B 420 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 435 " --> pdb=" O ASN B 430 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 379 through 380 Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.174A pdb=" N LEU C 316 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 428 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL C 318 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE C 426 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 391 through 394 removed outlier: 6.174A pdb=" N LEU C 316 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL C 428 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N VAL C 318 " --> pdb=" O PHE C 426 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE C 426 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 320 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE C 424 " --> pdb=" O ARG C 320 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 322 " --> pdb=" O THR C 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR C 422 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU C 324 " --> pdb=" O ARG C 420 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU C 435 " --> pdb=" O ASN C 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 379 through 380 Processing sheet with id=AA9, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.128A pdb=" N LEU D 316 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 428 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL D 318 " --> pdb=" O PHE D 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE D 426 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 391 through 394 removed outlier: 6.128A pdb=" N LEU D 316 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL D 428 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N VAL D 318 " --> pdb=" O PHE D 426 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE D 426 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG D 320 " --> pdb=" O ILE D 424 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 424 " --> pdb=" O ARG D 320 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ARG D 322 " --> pdb=" O THR D 422 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR D 422 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU D 324 " --> pdb=" O ARG D 420 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU D 435 " --> pdb=" O ASN D 430 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 379 through 380 839 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2396 1.31 - 1.43: 4858 1.43 - 1.56: 8785 1.56 - 1.69: 13 1.69 - 1.81: 124 Bond restraints: 16176 Sorted by residual: bond pdb=" C10 PEF A 801 " pdb=" O2 PEF A 801 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C10 PEF D 801 " pdb=" O2 PEF D 801 " ideal model delta sigma weight residual 1.330 1.399 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 PEF C 801 " pdb=" O2 PEF C 801 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C10 PEF B 801 " pdb=" O2 PEF B 801 " ideal model delta sigma weight residual 1.330 1.398 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C30 PEF B 801 " pdb=" O3 PEF B 801 " ideal model delta sigma weight residual 1.333 1.398 -0.065 2.00e-02 2.50e+03 1.07e+01 ... (remaining 16171 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 21758 3.21 - 6.42: 129 6.42 - 9.63: 21 9.63 - 12.84: 4 12.84 - 16.05: 4 Bond angle restraints: 21916 Sorted by residual: angle pdb=" CA PRO B 604 " pdb=" N PRO B 604 " pdb=" CD PRO B 604 " ideal model delta sigma weight residual 112.00 103.43 8.57 1.40e+00 5.10e-01 3.74e+01 angle pdb=" CA PRO C 604 " pdb=" N PRO C 604 " pdb=" CD PRO C 604 " ideal model delta sigma weight residual 112.00 103.63 8.37 1.40e+00 5.10e-01 3.57e+01 angle pdb=" CA PRO A 604 " pdb=" N PRO A 604 " pdb=" CD PRO A 604 " ideal model delta sigma weight residual 112.00 103.97 8.03 1.40e+00 5.10e-01 3.29e+01 angle pdb=" CA PRO D 604 " pdb=" N PRO D 604 " pdb=" CD PRO D 604 " ideal model delta sigma weight residual 112.00 104.05 7.95 1.40e+00 5.10e-01 3.22e+01 angle pdb=" O3P PEF C 801 " pdb=" P PEF C 801 " pdb=" O4P PEF C 801 " ideal model delta sigma weight residual 93.96 110.01 -16.05 3.00e+00 1.11e-01 2.86e+01 ... (remaining 21911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8622 17.99 - 35.99: 732 35.99 - 53.98: 167 53.98 - 71.97: 41 71.97 - 89.97: 10 Dihedral angle restraints: 9572 sinusoidal: 4048 harmonic: 5524 Sorted by residual: dihedral pdb=" CA ASP D 416 " pdb=" C ASP D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual 180.00 159.33 20.67 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA ASP C 416 " pdb=" C ASP C 416 " pdb=" N ARG C 417 " pdb=" CA ARG C 417 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 416 " pdb=" C ASP A 416 " pdb=" N ARG A 417 " pdb=" CA ARG A 417 " ideal model delta harmonic sigma weight residual 180.00 159.38 20.62 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 9569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2055 0.057 - 0.113: 351 0.113 - 0.170: 45 0.170 - 0.227: 3 0.227 - 0.283: 2 Chirality restraints: 2456 Sorted by residual: chirality pdb=" CA MET A 590 " pdb=" N MET A 590 " pdb=" C MET A 590 " pdb=" CB MET A 590 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA LEU D 586 " pdb=" N LEU D 586 " pdb=" C LEU D 586 " pdb=" CB LEU D 586 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA ILE C 679 " pdb=" N ILE C 679 " pdb=" C ILE C 679 " pdb=" CB ILE C 679 " both_signs ideal model delta sigma weight residual False 2.43 2.22 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2453 not shown) Planarity restraints: 2708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 603 " -0.088 5.00e-02 4.00e+02 1.29e-01 2.65e+01 pdb=" N PRO B 604 " 0.222 5.00e-02 4.00e+02 pdb=" CA PRO B 604 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 604 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 603 " -0.088 5.00e-02 4.00e+02 1.28e-01 2.60e+01 pdb=" N PRO C 604 " 0.220 5.00e-02 4.00e+02 pdb=" CA PRO C 604 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 604 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 603 " 0.085 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 604 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 604 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO A 604 " 0.066 5.00e-02 4.00e+02 ... (remaining 2705 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 29 2.32 - 2.96: 7513 2.96 - 3.61: 22261 3.61 - 4.25: 34431 4.25 - 4.90: 60785 Nonbonded interactions: 125019 Sorted by model distance: nonbonded pdb=" O SER D 587 " pdb=" OG SER D 591 " model vdw 1.671 3.040 nonbonded pdb=" OD1 ASN A 681 " pdb=" CG2 THR B 683 " model vdw 1.707 3.460 nonbonded pdb=" NH2 ARG D 440 " pdb=" N PEF D 801 " model vdw 1.750 2.560 nonbonded pdb=" OD1 ASN B 681 " pdb=" CG2 THR C 683 " model vdw 1.900 3.460 nonbonded pdb=" ND2 ASN A 674 " pdb=" CE MET B 590 " model vdw 1.927 3.540 ... (remaining 125014 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 215 through 804) 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: 1.240 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.000 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.010 0.830 16196 Z= 0.939 Angle : 0.760 16.047 21960 Z= 0.407 Chirality : 0.044 0.283 2456 Planarity : 0.006 0.129 2696 Dihedral : 14.320 89.967 5992 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 0.77 % Allowed : 1.18 % Favored : 98.05 % 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: -0.59 (0.20), residues: 1848 helix: 0.66 (0.17), residues: 972 sheet: -1.34 (0.36), residues: 200 loop : -1.57 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 306 TYR 0.017 0.001 TYR D 249 PHE 0.033 0.001 PHE C 600 TRP 0.017 0.001 TRP D 414 HIS 0.004 0.001 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00385 (16176) covalent geometry : angle 0.75717 (21916) SS BOND : bond 0.00333 ( 4) SS BOND : angle 1.81740 ( 8) hydrogen bonds : bond 0.16868 ( 797) hydrogen bonds : angle 5.92567 ( 2415) Misc. bond : bond 0.58516 ( 4) link_NAG-ASN : bond 0.00135 ( 12) link_NAG-ASN : angle 1.56814 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 340 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.6266 (pmm) cc_final: 0.5385 (tpt) REVERT: A 684 TYR cc_start: 0.5167 (OUTLIER) cc_final: 0.3338 (m-10) REVERT: B 583 MET cc_start: 0.5745 (pmm) cc_final: 0.5064 (tpt) REVERT: B 585 GLN cc_start: 0.7584 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: B 684 TYR cc_start: 0.5583 (OUTLIER) cc_final: 0.4750 (t80) REVERT: C 227 TYR cc_start: 0.7810 (t80) cc_final: 0.7604 (t80) REVERT: C 495 ILE cc_start: 0.8127 (tt) cc_final: 0.7911 (mt) REVERT: C 508 ASN cc_start: 0.8504 (m110) cc_final: 0.8196 (m-40) REVERT: C 583 MET cc_start: 0.5902 (pmm) cc_final: 0.5163 (tpt) REVERT: D 508 ASN cc_start: 0.8519 (m110) cc_final: 0.8296 (m-40) REVERT: D 583 MET cc_start: 0.6227 (pmm) cc_final: 0.5298 (tpt) outliers start: 13 outliers final: 6 residues processed: 353 average time/residue: 0.5317 time to fit residues: 210.0964 Evaluate side-chains 247 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 585 GLN Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.4980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN A 543 ASN B 305 ASN B 412 ASN B 543 ASN C 305 ASN C 412 ASN C 543 ASN D 305 ASN D 379 HIS D 412 ASN D 543 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.162691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112968 restraints weight = 18598.990| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.30 r_work: 0.3134 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16196 Z= 0.140 Angle : 0.606 7.460 21960 Z= 0.324 Chirality : 0.042 0.178 2456 Planarity : 0.006 0.196 2696 Dihedral : 9.963 86.339 2477 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.61 % Rotamer: Outliers : 2.96 % Allowed : 11.32 % Favored : 85.72 % 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: -0.25 (0.20), residues: 1848 helix: 1.03 (0.17), residues: 988 sheet: -0.97 (0.37), residues: 200 loop : -1.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG D 440 TYR 0.019 0.001 TYR A 249 PHE 0.021 0.001 PHE D 670 TRP 0.014 0.001 TRP D 414 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00302 (16176) covalent geometry : angle 0.60096 (21916) SS BOND : bond 0.00429 ( 4) SS BOND : angle 2.31791 ( 8) hydrogen bonds : bond 0.04822 ( 797) hydrogen bonds : angle 4.17572 ( 2415) Misc. bond : bond 0.00155 ( 4) link_NAG-ASN : bond 0.00118 ( 12) link_NAG-ASN : angle 1.69478 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 273 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7958 (t80) cc_final: 0.7674 (t80) REVERT: A 236 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 305 ASN cc_start: 0.7430 (p0) cc_final: 0.7052 (p0) REVERT: A 602 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.7737 (pp) REVERT: A 631 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7530 (mt-10) REVERT: A 684 TYR cc_start: 0.5177 (OUTLIER) cc_final: 0.3148 (m-10) REVERT: B 229 LEU cc_start: 0.8567 (mt) cc_final: 0.8301 (mp) REVERT: B 252 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8049 (mpp) REVERT: B 255 GLN cc_start: 0.8797 (mt0) cc_final: 0.8566 (mt0) REVERT: B 583 MET cc_start: 0.6087 (pmm) cc_final: 0.5253 (tpt) REVERT: B 586 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6629 (tp) REVERT: C 229 LEU cc_start: 0.8507 (mt) cc_final: 0.8255 (mp) REVERT: C 252 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8024 (mpp) REVERT: C 305 ASN cc_start: 0.7249 (OUTLIER) cc_final: 0.6977 (p0) REVERT: C 508 ASN cc_start: 0.8577 (m110) cc_final: 0.8241 (m-40) REVERT: C 583 MET cc_start: 0.5929 (pmm) cc_final: 0.5032 (tpt) REVERT: C 590 MET cc_start: 0.4926 (mtp) cc_final: 0.3861 (mmt) REVERT: D 252 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: D 255 GLN cc_start: 0.8824 (mt0) cc_final: 0.8577 (mt0) REVERT: D 508 ASN cc_start: 0.8567 (m110) cc_final: 0.8354 (m-40) REVERT: D 583 MET cc_start: 0.5758 (pmm) cc_final: 0.5069 (tpt) outliers start: 50 outliers final: 12 residues processed: 294 average time/residue: 0.4302 time to fit residues: 145.3747 Evaluate side-chains 262 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 586 LEU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 125 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 181 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 305 ASN B 543 ASN B 580 ASN C 543 ASN D 305 ASN D 543 ASN D 580 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.157117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.107154 restraints weight = 18632.426| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.30 r_work: 0.3053 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16196 Z= 0.214 Angle : 0.680 7.809 21960 Z= 0.361 Chirality : 0.045 0.184 2456 Planarity : 0.005 0.120 2696 Dihedral : 9.388 88.341 2466 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.60 % Favored : 93.18 % Rotamer: Outliers : 4.21 % Allowed : 14.10 % Favored : 81.69 % 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 (0.20), residues: 1848 helix: 1.10 (0.17), residues: 984 sheet: -1.04 (0.36), residues: 200 loop : -1.63 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 440 TYR 0.026 0.002 TYR A 249 PHE 0.021 0.002 PHE B 600 TRP 0.015 0.002 TRP A 414 HIS 0.003 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00510 (16176) covalent geometry : angle 0.67223 (21916) SS BOND : bond 0.00711 ( 4) SS BOND : angle 3.35304 ( 8) hydrogen bonds : bond 0.05703 ( 797) hydrogen bonds : angle 4.12274 ( 2415) Misc. bond : bond 0.00164 ( 4) link_NAG-ASN : bond 0.00190 ( 12) link_NAG-ASN : angle 2.12397 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 271 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8087 (t80) cc_final: 0.7533 (t80) REVERT: A 252 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8137 (mpp) REVERT: A 305 ASN cc_start: 0.7459 (p0) cc_final: 0.7039 (p0) REVERT: A 511 ASP cc_start: 0.7566 (m-30) cc_final: 0.7364 (m-30) REVERT: A 583 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.4725 (tpt) REVERT: A 628 THR cc_start: 0.8198 (p) cc_final: 0.7687 (p) REVERT: A 631 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7226 (mt-10) REVERT: A 651 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 684 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.3151 (m-10) REVERT: B 252 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8140 (mpp) REVERT: B 305 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6740 (p0) REVERT: B 583 MET cc_start: 0.6252 (pmm) cc_final: 0.5380 (tpt) REVERT: B 602 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8084 (pp) REVERT: B 651 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7636 (tm-30) REVERT: C 252 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: C 583 MET cc_start: 0.6079 (pmm) cc_final: 0.5110 (tpt) REVERT: C 590 MET cc_start: 0.4809 (mtp) cc_final: 0.4164 (mtm) REVERT: C 603 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7467 (ttt) REVERT: C 650 GLU cc_start: 0.8368 (tp30) cc_final: 0.7798 (pt0) REVERT: C 651 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: D 252 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: D 305 ASN cc_start: 0.7035 (OUTLIER) cc_final: 0.6749 (p0) REVERT: D 538 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7831 (t80) REVERT: D 583 MET cc_start: 0.5918 (pmm) cc_final: 0.5142 (tpt) REVERT: D 602 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7912 (pp) REVERT: D 603 MET cc_start: 0.7950 (ttt) cc_final: 0.7746 (ttt) outliers start: 71 outliers final: 17 residues processed: 302 average time/residue: 0.4742 time to fit residues: 162.7089 Evaluate side-chains 273 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 241 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 603 MET Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 5 optimal weight: 6.9990 chunk 177 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 157 optimal weight: 0.3980 chunk 123 optimal weight: 7.9990 chunk 133 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 543 ASN B 255 GLN B 543 ASN C 508 ASN C 543 ASN D 255 GLN D 508 ASN D 543 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.111914 restraints weight = 18493.885| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.28 r_work: 0.3125 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16196 Z= 0.124 Angle : 0.583 7.455 21960 Z= 0.312 Chirality : 0.041 0.157 2456 Planarity : 0.006 0.207 2696 Dihedral : 8.717 89.120 2462 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.01 % Favored : 93.78 % Rotamer: Outliers : 2.73 % Allowed : 17.06 % Favored : 80.21 % 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: 0.05 (0.20), residues: 1848 helix: 1.39 (0.17), residues: 960 sheet: -0.97 (0.37), residues: 200 loop : -1.63 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D 440 TYR 0.013 0.001 TYR B 249 PHE 0.023 0.001 PHE A 670 TRP 0.013 0.001 TRP D 414 HIS 0.001 0.000 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00265 (16176) covalent geometry : angle 0.57833 (21916) SS BOND : bond 0.00374 ( 4) SS BOND : angle 2.31820 ( 8) hydrogen bonds : bond 0.04454 ( 797) hydrogen bonds : angle 3.85531 ( 2415) Misc. bond : bond 0.00304 ( 4) link_NAG-ASN : bond 0.00130 ( 12) link_NAG-ASN : angle 1.61805 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 268 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8017 (t80) cc_final: 0.7642 (t80) REVERT: A 305 ASN cc_start: 0.7367 (p0) cc_final: 0.6957 (p0) REVERT: A 583 MET cc_start: 0.6086 (pmt) cc_final: 0.4838 (tpt) REVERT: A 590 MET cc_start: 0.6585 (mmt) cc_final: 0.6027 (ptt) REVERT: A 602 ILE cc_start: 0.8017 (OUTLIER) cc_final: 0.7770 (pp) REVERT: A 631 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7397 (mt-10) REVERT: A 651 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7452 (tm-30) REVERT: A 684 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.3115 (m-10) REVERT: B 251 ARG cc_start: 0.8859 (ttt90) cc_final: 0.8618 (ttt90) REVERT: B 343 GLU cc_start: 0.8610 (mp0) cc_final: 0.7961 (mm-30) REVERT: B 583 MET cc_start: 0.6171 (pmm) cc_final: 0.5208 (tpt) REVERT: B 651 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: C 251 ARG cc_start: 0.8919 (ttt90) cc_final: 0.8696 (ttt90) REVERT: C 305 ASN cc_start: 0.6888 (p0) cc_final: 0.6193 (p0) REVERT: C 583 MET cc_start: 0.6033 (pmm) cc_final: 0.5027 (tpt) REVERT: C 590 MET cc_start: 0.4621 (mtp) cc_final: 0.4007 (mtm) REVERT: C 602 ILE cc_start: 0.7925 (OUTLIER) cc_final: 0.7692 (pp) REVERT: C 603 MET cc_start: 0.7466 (ttp) cc_final: 0.7166 (ttt) REVERT: C 651 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: D 583 MET cc_start: 0.5686 (pmm) cc_final: 0.4822 (tpt) outliers start: 46 outliers final: 12 residues processed: 287 average time/residue: 0.4858 time to fit residues: 157.7914 Evaluate side-chains 258 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 59 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.158735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.109106 restraints weight = 18530.664| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 2.27 r_work: 0.3079 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16196 Z= 0.166 Angle : 0.633 8.355 21960 Z= 0.334 Chirality : 0.043 0.158 2456 Planarity : 0.007 0.271 2696 Dihedral : 8.545 86.685 2462 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 3.61 % Allowed : 17.36 % Favored : 79.03 % 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: 0.05 (0.20), residues: 1848 helix: 1.39 (0.17), residues: 964 sheet: -0.97 (0.37), residues: 200 loop : -1.64 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 440 TYR 0.018 0.002 TYR A 249 PHE 0.021 0.001 PHE B 600 TRP 0.011 0.001 TRP C 414 HIS 0.002 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00387 (16176) covalent geometry : angle 0.62639 (21916) SS BOND : bond 0.00529 ( 4) SS BOND : angle 2.80533 ( 8) hydrogen bonds : bond 0.05056 ( 797) hydrogen bonds : angle 3.91086 ( 2415) Misc. bond : bond 0.00337 ( 4) link_NAG-ASN : bond 0.00104 ( 12) link_NAG-ASN : angle 1.89335 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 259 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8020 (t80) cc_final: 0.7634 (t80) REVERT: A 251 ARG cc_start: 0.8957 (ttt90) cc_final: 0.8670 (ttt90) REVERT: A 252 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8165 (mpp) REVERT: A 305 ASN cc_start: 0.7415 (p0) cc_final: 0.6936 (p0) REVERT: A 583 MET cc_start: 0.6061 (OUTLIER) cc_final: 0.4631 (tpt) REVERT: A 590 MET cc_start: 0.6465 (mmt) cc_final: 0.6025 (ptm) REVERT: A 602 ILE cc_start: 0.8019 (OUTLIER) cc_final: 0.7779 (pp) REVERT: A 631 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7358 (mt-10) REVERT: A 651 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: A 684 TYR cc_start: 0.5084 (OUTLIER) cc_final: 0.3111 (m-10) REVERT: B 251 ARG cc_start: 0.8893 (ttt90) cc_final: 0.8647 (ttt90) REVERT: B 252 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8158 (mpp) REVERT: B 583 MET cc_start: 0.6022 (pmm) cc_final: 0.5002 (tpt) REVERT: B 590 MET cc_start: 0.3812 (mtp) cc_final: 0.3250 (mtm) REVERT: B 602 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8030 (pp) REVERT: B 651 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: C 251 ARG cc_start: 0.8921 (ttt90) cc_final: 0.8664 (ttt90) REVERT: C 252 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8104 (mpp) REVERT: C 305 ASN cc_start: 0.6788 (p0) cc_final: 0.5978 (p0) REVERT: C 583 MET cc_start: 0.6054 (pmm) cc_final: 0.4979 (tpt) REVERT: C 590 MET cc_start: 0.4698 (mtp) cc_final: 0.3731 (ptm) REVERT: C 602 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7770 (pp) REVERT: C 603 MET cc_start: 0.7643 (ttp) cc_final: 0.7208 (ttt) REVERT: C 651 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: D 251 ARG cc_start: 0.8928 (ttt90) cc_final: 0.8680 (ttt90) REVERT: D 252 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8144 (mpp) REVERT: D 538 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7839 (t80) REVERT: D 583 MET cc_start: 0.5847 (pmm) cc_final: 0.4880 (tpt) REVERT: D 590 MET cc_start: 0.5890 (ptt) cc_final: 0.5083 (ppp) REVERT: D 603 MET cc_start: 0.7544 (ttp) cc_final: 0.7030 (ttt) outliers start: 61 outliers final: 23 residues processed: 282 average time/residue: 0.4698 time to fit residues: 150.4918 Evaluate side-chains 275 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 239 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 602 ILE Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 582 THR Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 75 optimal weight: 0.4980 chunk 139 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.159422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.109873 restraints weight = 18489.473| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.27 r_work: 0.3096 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16196 Z= 0.152 Angle : 0.612 7.450 21960 Z= 0.324 Chirality : 0.042 0.154 2456 Planarity : 0.006 0.197 2696 Dihedral : 8.325 86.147 2462 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.76 % Favored : 93.02 % Rotamer: Outliers : 3.32 % Allowed : 18.13 % Favored : 78.55 % 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: 0.06 (0.20), residues: 1848 helix: 1.38 (0.17), residues: 972 sheet: -0.99 (0.37), residues: 200 loop : -1.64 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 440 TYR 0.017 0.001 TYR A 527 PHE 0.025 0.002 PHE A 670 TRP 0.011 0.001 TRP D 414 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00350 (16176) covalent geometry : angle 0.60577 (21916) SS BOND : bond 0.00528 ( 4) SS BOND : angle 2.61445 ( 8) hydrogen bonds : bond 0.04858 ( 797) hydrogen bonds : angle 3.86007 ( 2415) Misc. bond : bond 0.00232 ( 4) link_NAG-ASN : bond 0.00039 ( 12) link_NAG-ASN : angle 1.78895 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 257 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8011 (t80) cc_final: 0.7691 (t80) REVERT: A 251 ARG cc_start: 0.8944 (ttt90) cc_final: 0.8669 (ttt90) REVERT: A 252 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8159 (mpp) REVERT: A 305 ASN cc_start: 0.7374 (p0) cc_final: 0.6974 (p0) REVERT: A 583 MET cc_start: 0.6073 (OUTLIER) cc_final: 0.4554 (tpt) REVERT: A 590 MET cc_start: 0.6496 (mmt) cc_final: 0.6051 (ptm) REVERT: A 631 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 651 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: A 684 TYR cc_start: 0.5044 (OUTLIER) cc_final: 0.3142 (m-10) REVERT: B 251 ARG cc_start: 0.8888 (ttt90) cc_final: 0.8646 (ttt90) REVERT: B 252 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8147 (mpp) REVERT: B 305 ASN cc_start: 0.6906 (p0) cc_final: 0.6169 (p0) REVERT: B 455 TRP cc_start: 0.8406 (OUTLIER) cc_final: 0.7722 (p90) REVERT: B 543 ASN cc_start: 0.8832 (OUTLIER) cc_final: 0.8587 (t0) REVERT: B 583 MET cc_start: 0.5997 (pmm) cc_final: 0.4948 (tpp) REVERT: B 590 MET cc_start: 0.3815 (mtp) cc_final: 0.3173 (mtm) REVERT: B 602 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7923 (pp) REVERT: B 651 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: C 251 ARG cc_start: 0.8915 (ttt90) cc_final: 0.8673 (ttt90) REVERT: C 252 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8170 (mpp) REVERT: C 305 ASN cc_start: 0.6853 (p0) cc_final: 0.5971 (p0) REVERT: C 543 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8592 (t0) REVERT: C 583 MET cc_start: 0.5926 (pmm) cc_final: 0.4823 (tpt) REVERT: C 590 MET cc_start: 0.4604 (mtp) cc_final: 0.3648 (ptm) REVERT: C 602 ILE cc_start: 0.8047 (OUTLIER) cc_final: 0.7784 (pp) REVERT: C 603 MET cc_start: 0.7704 (ttp) cc_final: 0.7246 (ttt) REVERT: C 651 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7485 (tm-30) REVERT: D 251 ARG cc_start: 0.8927 (ttt90) cc_final: 0.8693 (ttt90) REVERT: D 252 MET cc_start: 0.8735 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: D 538 PHE cc_start: 0.8141 (OUTLIER) cc_final: 0.7814 (t80) REVERT: D 543 ASN cc_start: 0.8815 (OUTLIER) cc_final: 0.8582 (t0) REVERT: D 583 MET cc_start: 0.5957 (pmm) cc_final: 0.4992 (tpt) REVERT: D 590 MET cc_start: 0.5951 (ptt) cc_final: 0.5022 (ppp) REVERT: D 603 MET cc_start: 0.7516 (ttp) cc_final: 0.6953 (ttt) outliers start: 56 outliers final: 24 residues processed: 278 average time/residue: 0.4931 time to fit residues: 155.0708 Evaluate side-chains 287 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 54 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.157893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.108262 restraints weight = 18441.513| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.26 r_work: 0.3072 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16196 Z= 0.188 Angle : 0.657 9.673 21960 Z= 0.346 Chirality : 0.044 0.160 2456 Planarity : 0.006 0.180 2696 Dihedral : 8.388 86.523 2462 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.09 % Favored : 92.69 % Rotamer: Outliers : 3.67 % Allowed : 18.25 % Favored : 78.08 % 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: 0.02 (0.20), residues: 1848 helix: 1.31 (0.17), residues: 976 sheet: -1.02 (0.37), residues: 200 loop : -1.62 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 440 TYR 0.017 0.002 TYR B 249 PHE 0.022 0.002 PHE B 600 TRP 0.009 0.001 TRP A 414 HIS 0.002 0.001 HIS D 498 Details of bonding type rmsd covalent geometry : bond 0.00444 (16176) covalent geometry : angle 0.65057 (21916) SS BOND : bond 0.00640 ( 4) SS BOND : angle 2.99866 ( 8) hydrogen bonds : bond 0.05286 ( 797) hydrogen bonds : angle 3.93107 ( 2415) Misc. bond : bond 0.00239 ( 4) link_NAG-ASN : bond 0.00165 ( 12) link_NAG-ASN : angle 1.99232 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 255 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8007 (t80) cc_final: 0.7707 (t80) REVERT: A 241 MET cc_start: 0.7326 (mtt) cc_final: 0.7072 (mpm) REVERT: A 251 ARG cc_start: 0.8976 (ttt90) cc_final: 0.8707 (ttt90) REVERT: A 252 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: A 305 ASN cc_start: 0.7376 (p0) cc_final: 0.6865 (p0) REVERT: A 543 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8532 (t0) REVERT: A 583 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.4535 (tpt) REVERT: A 590 MET cc_start: 0.6536 (mmt) cc_final: 0.6066 (ptm) REVERT: A 628 THR cc_start: 0.8015 (p) cc_final: 0.7475 (t) REVERT: A 631 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7486 (mt-10) REVERT: A 651 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: A 684 TYR cc_start: 0.5115 (OUTLIER) cc_final: 0.3232 (m-10) REVERT: B 251 ARG cc_start: 0.8915 (ttt90) cc_final: 0.8666 (ttt90) REVERT: B 252 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8183 (mpp) REVERT: B 305 ASN cc_start: 0.6843 (p0) cc_final: 0.6009 (p0) REVERT: B 312 GLU cc_start: 0.8183 (pm20) cc_final: 0.7896 (pm20) REVERT: B 455 TRP cc_start: 0.8463 (OUTLIER) cc_final: 0.7702 (p90) REVERT: B 543 ASN cc_start: 0.8854 (OUTLIER) cc_final: 0.8571 (t0) REVERT: B 583 MET cc_start: 0.5991 (pmm) cc_final: 0.4958 (tpp) REVERT: B 590 MET cc_start: 0.3918 (mtp) cc_final: 0.3487 (mtm) REVERT: B 602 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7971 (pp) REVERT: B 651 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7667 (tm-30) REVERT: C 252 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: C 305 ASN cc_start: 0.6805 (p0) cc_final: 0.5847 (p0) REVERT: C 543 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8566 (t0) REVERT: C 583 MET cc_start: 0.5927 (pmm) cc_final: 0.4780 (tpt) REVERT: C 590 MET cc_start: 0.4847 (mtp) cc_final: 0.3783 (ptm) REVERT: C 603 MET cc_start: 0.7852 (ttp) cc_final: 0.7401 (ttt) REVERT: C 651 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: D 251 ARG cc_start: 0.8945 (ttt90) cc_final: 0.8703 (ttt90) REVERT: D 252 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8156 (mpp) REVERT: D 538 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7851 (t80) REVERT: D 543 ASN cc_start: 0.8840 (OUTLIER) cc_final: 0.8559 (t0) REVERT: D 583 MET cc_start: 0.5852 (pmm) cc_final: 0.4958 (tpt) REVERT: D 590 MET cc_start: 0.5923 (ptt) cc_final: 0.4994 (ppp) REVERT: D 602 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7932 (pp) REVERT: D 603 MET cc_start: 0.7669 (ttp) cc_final: 0.7105 (ttt) outliers start: 62 outliers final: 28 residues processed: 284 average time/residue: 0.4849 time to fit residues: 156.1870 Evaluate side-chains 289 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 425 ASP Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 677 LEU Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.158343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.109135 restraints weight = 18553.394| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.25 r_work: 0.3083 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16196 Z= 0.158 Angle : 0.635 12.756 21960 Z= 0.334 Chirality : 0.043 0.148 2456 Planarity : 0.006 0.244 2696 Dihedral : 8.282 84.510 2462 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.71 % Favored : 93.07 % Rotamer: Outliers : 3.61 % Allowed : 18.36 % Favored : 78.02 % 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: 0.05 (0.20), residues: 1848 helix: 1.34 (0.17), residues: 976 sheet: -1.06 (0.37), residues: 200 loop : -1.57 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG D 440 TYR 0.016 0.001 TYR C 527 PHE 0.027 0.002 PHE A 670 TRP 0.009 0.001 TRP A 414 HIS 0.002 0.001 HIS C 498 Details of bonding type rmsd covalent geometry : bond 0.00364 (16176) covalent geometry : angle 0.62897 (21916) SS BOND : bond 0.00549 ( 4) SS BOND : angle 2.76545 ( 8) hydrogen bonds : bond 0.05017 ( 797) hydrogen bonds : angle 3.88754 ( 2415) Misc. bond : bond 0.00269 ( 4) link_NAG-ASN : bond 0.00048 ( 12) link_NAG-ASN : angle 1.84408 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 0.539 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 227 TYR cc_start: 0.7984 (t80) cc_final: 0.7679 (t80) REVERT: A 251 ARG cc_start: 0.8922 (ttt90) cc_final: 0.8700 (ttt90) REVERT: A 252 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8114 (mpp) REVERT: A 305 ASN cc_start: 0.7334 (p0) cc_final: 0.6902 (p0) REVERT: A 583 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.4541 (tpt) REVERT: A 590 MET cc_start: 0.6585 (mmt) cc_final: 0.6322 (pp-130) REVERT: A 631 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7389 (mt-10) REVERT: A 651 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: A 684 TYR cc_start: 0.5138 (OUTLIER) cc_final: 0.3242 (m-10) REVERT: B 251 ARG cc_start: 0.8877 (ttt90) cc_final: 0.8633 (ttt90) REVERT: B 252 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8153 (mpp) REVERT: B 305 ASN cc_start: 0.6879 (p0) cc_final: 0.6018 (p0) REVERT: B 455 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.7665 (p90) REVERT: B 543 ASN cc_start: 0.8807 (OUTLIER) cc_final: 0.8532 (t0) REVERT: B 583 MET cc_start: 0.6003 (pmm) cc_final: 0.4946 (tpp) REVERT: B 590 MET cc_start: 0.3946 (mtp) cc_final: 0.3489 (mtm) REVERT: B 602 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7977 (pp) REVERT: B 651 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: C 252 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: C 305 ASN cc_start: 0.6974 (p0) cc_final: 0.5917 (p0) REVERT: C 543 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8539 (t0) REVERT: C 583 MET cc_start: 0.5952 (pmm) cc_final: 0.4815 (tpt) REVERT: C 590 MET cc_start: 0.4916 (mtp) cc_final: 0.3649 (ptm) REVERT: C 602 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7821 (pp) REVERT: C 603 MET cc_start: 0.7786 (ttp) cc_final: 0.7287 (ttt) REVERT: C 651 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: D 251 ARG cc_start: 0.8898 (ttt90) cc_final: 0.8663 (ttt90) REVERT: D 252 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: D 538 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7874 (t80) REVERT: D 543 ASN cc_start: 0.8810 (OUTLIER) cc_final: 0.8534 (t0) REVERT: D 583 MET cc_start: 0.5896 (pmm) cc_final: 0.5007 (tpt) REVERT: D 590 MET cc_start: 0.5988 (ptt) cc_final: 0.5092 (ppp) REVERT: D 603 MET cc_start: 0.7596 (ttp) cc_final: 0.7079 (ttt) outliers start: 61 outliers final: 27 residues processed: 273 average time/residue: 0.4480 time to fit residues: 139.3763 Evaluate side-chains 280 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 237 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 651 GLU Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 602 ILE Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 178 optimal weight: 0.9980 chunk 174 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN B 543 ASN C 255 GLN C 543 ASN D 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.110354 restraints weight = 18517.374| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.28 r_work: 0.3106 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16196 Z= 0.139 Angle : 0.623 11.838 21960 Z= 0.327 Chirality : 0.042 0.181 2456 Planarity : 0.006 0.207 2696 Dihedral : 8.099 85.014 2462 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.87 % Favored : 92.91 % Rotamer: Outliers : 3.14 % Allowed : 19.19 % Favored : 77.67 % 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 (0.20), residues: 1848 helix: 1.43 (0.17), residues: 972 sheet: -1.05 (0.37), residues: 200 loop : -1.59 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 440 TYR 0.015 0.001 TYR A 527 PHE 0.023 0.001 PHE B 600 TRP 0.009 0.001 TRP A 414 HIS 0.001 0.001 HIS D 379 Details of bonding type rmsd covalent geometry : bond 0.00310 (16176) covalent geometry : angle 0.61764 (21916) SS BOND : bond 0.00472 ( 4) SS BOND : angle 2.46438 ( 8) hydrogen bonds : bond 0.04691 ( 797) hydrogen bonds : angle 3.83324 ( 2415) Misc. bond : bond 0.00234 ( 4) link_NAG-ASN : bond 0.00045 ( 12) link_NAG-ASN : angle 1.70657 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 249 time to evaluate : 0.611 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 227 TYR cc_start: 0.7955 (t80) cc_final: 0.7711 (t80) REVERT: A 251 ARG cc_start: 0.8885 (ttt90) cc_final: 0.8654 (ttt90) REVERT: A 252 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8125 (mpp) REVERT: A 305 ASN cc_start: 0.7345 (p0) cc_final: 0.6895 (p0) REVERT: A 538 PHE cc_start: 0.8202 (OUTLIER) cc_final: 0.7902 (t80) REVERT: A 583 MET cc_start: 0.5876 (OUTLIER) cc_final: 0.4547 (tpt) REVERT: A 590 MET cc_start: 0.6576 (mmt) cc_final: 0.6331 (pp-130) REVERT: A 631 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7494 (mt-10) REVERT: A 651 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7241 (tm-30) REVERT: A 684 TYR cc_start: 0.5029 (OUTLIER) cc_final: 0.3164 (m-10) REVERT: B 251 ARG cc_start: 0.8863 (ttt90) cc_final: 0.8630 (ttt90) REVERT: B 252 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8181 (mpp) REVERT: B 305 ASN cc_start: 0.6877 (p0) cc_final: 0.6044 (p0) REVERT: B 455 TRP cc_start: 0.8438 (OUTLIER) cc_final: 0.7674 (p90) REVERT: B 543 ASN cc_start: 0.8829 (OUTLIER) cc_final: 0.8562 (t0) REVERT: B 583 MET cc_start: 0.6020 (pmm) cc_final: 0.4975 (tpp) REVERT: B 590 MET cc_start: 0.3941 (mtp) cc_final: 0.3478 (mtm) REVERT: B 602 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7950 (pp) REVERT: C 252 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8127 (mpp) REVERT: C 305 ASN cc_start: 0.7049 (p0) cc_final: 0.5959 (p0) REVERT: C 543 ASN cc_start: 0.8814 (OUTLIER) cc_final: 0.8542 (t0) REVERT: C 583 MET cc_start: 0.5901 (pmm) cc_final: 0.4788 (tpt) REVERT: C 590 MET cc_start: 0.4755 (mtp) cc_final: 0.3534 (ptm) REVERT: C 603 MET cc_start: 0.7744 (ttp) cc_final: 0.7244 (ttt) REVERT: D 251 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8663 (ttt90) REVERT: D 252 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8170 (mpp) REVERT: D 538 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7857 (t80) REVERT: D 543 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8611 (t0) REVERT: D 583 MET cc_start: 0.6037 (pmm) cc_final: 0.5168 (tpt) REVERT: D 590 MET cc_start: 0.5866 (ptt) cc_final: 0.5026 (ppp) REVERT: D 603 MET cc_start: 0.7529 (ttp) cc_final: 0.6960 (ttt) outliers start: 53 outliers final: 27 residues processed: 273 average time/residue: 0.4886 time to fit residues: 150.9985 Evaluate side-chains 277 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 236 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 500 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 624 ASP Chi-restraints excluded: chain A residue 651 GLU Chi-restraints excluded: chain A residue 677 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 464 ARG Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 543 ASN Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 624 ASP Chi-restraints excluded: chain C residue 653 ASN Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 464 ARG Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 543 ASN Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 684 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 181 optimal weight: 0.0670 chunk 19 optimal weight: 0.0270 chunk 59 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 125 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 151 optimal weight: 0.0270 chunk 57 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 543 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.164164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.115890 restraints weight = 18432.734| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.26 r_work: 0.3189 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16196 Z= 0.111 Angle : 0.589 11.339 21960 Z= 0.309 Chirality : 0.041 0.165 2456 Planarity : 0.005 0.166 2696 Dihedral : 7.735 88.281 2462 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 1.54 % Allowed : 20.97 % Favored : 77.49 % 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 (0.20), residues: 1848 helix: 1.64 (0.17), residues: 960 sheet: -0.88 (0.38), residues: 200 loop : -1.69 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 251 TYR 0.011 0.001 TYR A 527 PHE 0.028 0.001 PHE A 670 TRP 0.010 0.001 TRP A 414 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00226 (16176) covalent geometry : angle 0.58642 (21916) SS BOND : bond 0.00180 ( 4) SS BOND : angle 1.48221 ( 8) hydrogen bonds : bond 0.03755 ( 797) hydrogen bonds : angle 3.69301 ( 2415) Misc. bond : bond 0.00170 ( 4) link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 1.39233 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3696 Ramachandran restraints generated. 1848 Oldfield, 0 Emsley, 1848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 261 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7924 (t80) cc_final: 0.7709 (t80) REVERT: A 305 ASN cc_start: 0.7265 (p0) cc_final: 0.6821 (p0) REVERT: A 343 GLU cc_start: 0.8350 (mp0) cc_final: 0.7815 (mm-30) REVERT: A 543 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8495 (t0) REVERT: A 583 MET cc_start: 0.5809 (OUTLIER) cc_final: 0.4557 (tpt) REVERT: A 590 MET cc_start: 0.6739 (mmt) cc_final: 0.6363 (pp-130) REVERT: B 305 ASN cc_start: 0.6966 (p0) cc_final: 0.6132 (p0) REVERT: B 455 TRP cc_start: 0.8414 (OUTLIER) cc_final: 0.7766 (p90) REVERT: B 583 MET cc_start: 0.5790 (pmm) cc_final: 0.4844 (tpp) REVERT: B 590 MET cc_start: 0.3968 (mtp) cc_final: 0.3543 (mtm) REVERT: B 602 ILE cc_start: 0.8088 (OUTLIER) cc_final: 0.7668 (tp) REVERT: C 305 ASN cc_start: 0.7016 (p0) cc_final: 0.5908 (p0) REVERT: C 583 MET cc_start: 0.5890 (pmm) cc_final: 0.4759 (tpt) REVERT: C 590 MET cc_start: 0.4386 (mtp) cc_final: 0.3323 (ptm) REVERT: C 603 MET cc_start: 0.7489 (ttp) cc_final: 0.7259 (ttp) REVERT: D 343 GLU cc_start: 0.8332 (mp0) cc_final: 0.7809 (mm-30) REVERT: D 538 PHE cc_start: 0.8095 (OUTLIER) cc_final: 0.7790 (t80) REVERT: D 583 MET cc_start: 0.5986 (pmm) cc_final: 0.5063 (tpt) REVERT: D 590 MET cc_start: 0.5904 (ptt) cc_final: 0.5088 (ppp) REVERT: D 603 MET cc_start: 0.7409 (ttp) cc_final: 0.7057 (ttm) outliers start: 26 outliers final: 12 residues processed: 266 average time/residue: 0.4465 time to fit residues: 135.0747 Evaluate side-chains 258 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 ARG Chi-restraints excluded: chain A residue 482 PHE Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 543 ASN Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 455 TRP Chi-restraints excluded: chain B residue 482 PHE Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain C residue 482 PHE Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 624 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 94 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 543 ASN B 255 GLN B 543 ASN C 543 ASN D 255 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.162360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.113446 restraints weight = 18445.880| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.26 r_work: 0.3167 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16196 Z= 0.121 Angle : 0.615 14.412 21960 Z= 0.320 Chirality : 0.042 0.184 2456 Planarity : 0.005 0.140 2696 Dihedral : 7.700 86.460 2460 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.48 % Allowed : 22.27 % Favored : 76.24 % 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: 0.30 (0.20), residues: 1848 helix: 1.67 (0.17), residues: 960 sheet: -0.84 (0.37), residues: 200 loop : -1.64 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 251 TYR 0.010 0.001 TYR A 249 PHE 0.024 0.001 PHE C 485 TRP 0.009 0.001 TRP A 414 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd covalent geometry : bond 0.00262 (16176) covalent geometry : angle 0.61206 (21916) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.65280 ( 8) hydrogen bonds : bond 0.04003 ( 797) hydrogen bonds : angle 3.70157 ( 2415) Misc. bond : bond 0.00147 ( 4) link_NAG-ASN : bond 0.00082 ( 12) link_NAG-ASN : angle 1.48233 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5598.08 seconds wall clock time: 96 minutes 2.98 seconds (5762.98 seconds total)