Starting phenix.real_space_refine on Fri Jul 3 20:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k3s_36858/07_2026/8k3s_36858_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k3s_36858/07_2026/8k3s_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 { model { file = "/net/cci-nas-00/data/ceres_data/8k3s_36858/07_2026/8k3s_36858_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k3s_36858/07_2026/8k3s_36858_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k3s_36858/07_2026/8k3s_36858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k3s_36858/07_2026/8k3s_36858.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 84 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 3, 'PEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 1 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: 3.71, per 1000 atoms: 0.24 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: 0.99 Conformation dependent library (CDL) restraints added in 666.9 milliseconds 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: 0.51 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: 2.32 Time building geometry restraints manager: 1.40 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.510 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 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 are 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/Z covalent geometry : bond 0.00385 / 0.19 (16176) covalent geometry : angle 0.75717 / 0.41 (21916) SS BOND : bond 0.00333 / 0.18 ( 4) SS BOND : angle 1.81740 / 0.89 ( 8) hydrogen bonds : bond 0.16868 / 10.99 ( 797) hydrogen bonds : angle 5.92567 / 3.95 ( 2415) Misc. bond : bond 0.58516 / 30.38 ( 4) link_NAG-ASN : bond 0.00135 / 0.08 ( 12) link_NAG-ASN : angle 1.56814 / 0.99 ( 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 : 0.583 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: 0.8503 (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: 0.4455 time to fit residues: 176.8087 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 : 0.458 ------------------------------------------------------------------------------- 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... A 412 ASN A 543 ASN B 305 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112940 restraints weight = 18535.346| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.27 r_work: 0.3145 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1437 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= 0.137 Angle : 0.607 7.518 21960 Z= 0.324 Chirality : 0.042 0.177 2456 Planarity : 0.006 0.202 2696 Dihedral : 10.091 89.512 2477 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.28 % Favored : 93.51 % Rotamer: Outliers : 2.84 % Allowed : 11.67 % Favored : 85.49 % 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 are not related in a simple way. whole: -0.24 (0.20), residues: 1848 helix: 1.04 (0.17), residues: 988 sheet: -0.96 (0.37), residues: 200 loop : -1.75 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.000 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/Z covalent geometry : bond 0.00298 / 0.14 (16176) covalent geometry : angle 0.60195 / 0.32 (21916) SS BOND : bond 0.00422 / 0.24 ( 4) SS BOND : angle 2.29338 / 1.13 ( 8) hydrogen bonds : bond 0.04862 / 3.09 ( 797) hydrogen bonds : angle 4.20060 / 2.85 ( 2415) Misc. bond : bond 0.00293 / 0.21 ( 4) link_NAG-ASN : bond 0.00096 / 0.06 ( 12) link_NAG-ASN : angle 1.66380 / 1.07 ( 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 320 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 272 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7949 (t80) cc_final: 0.7666 (t80) REVERT: A 236 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8882 (tp) REVERT: A 305 ASN cc_start: 0.7415 (p0) cc_final: 0.7047 (p0) REVERT: A 602 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7732 (pp) REVERT: A 631 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 684 TYR cc_start: 0.5209 (OUTLIER) cc_final: 0.3160 (m-10) REVERT: B 229 LEU cc_start: 0.8566 (mt) cc_final: 0.8299 (mp) REVERT: B 252 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8046 (mpp) REVERT: B 255 GLN cc_start: 0.8792 (mt0) cc_final: 0.8568 (mt0) REVERT: B 583 MET cc_start: 0.6073 (pmm) cc_final: 0.5248 (tpt) REVERT: B 586 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6601 (OUTLIER) REVERT: C 229 LEU cc_start: 0.8500 (mt) cc_final: 0.8243 (mp) REVERT: C 252 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8011 (mpp) REVERT: C 305 ASN cc_start: 0.7225 (OUTLIER) cc_final: 0.6956 (p0) REVERT: C 508 ASN cc_start: 0.8589 (m110) cc_final: 0.8259 (m-40) REVERT: C 583 MET cc_start: 0.5931 (pmm) cc_final: 0.5040 (tpt) REVERT: D 252 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8076 (mpp) REVERT: D 255 GLN cc_start: 0.8818 (mt0) cc_final: 0.8579 (mt0) REVERT: D 508 ASN cc_start: 0.8570 (m110) cc_final: 0.8354 (m-40) REVERT: D 583 MET cc_start: 0.5771 (pmm) cc_final: 0.5075 (tpt) outliers start: 48 outliers final: 12 residues processed: 293 average time/residue: 0.3933 time to fit residues: 133.0106 Evaluate side-chains 263 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.617 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 82 optimal weight: 3.9990 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: 2.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 181 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 305 ASN B 412 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.156050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.106388 restraints weight = 18646.926| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.27 r_work: 0.3041 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16196 Z= 0.230 Angle : 0.704 7.819 21960 Z= 0.373 Chirality : 0.046 0.187 2456 Planarity : 0.005 0.125 2696 Dihedral : 9.442 88.488 2466 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.60 % Favored : 93.18 % Rotamer: Outliers : 3.97 % Allowed : 14.75 % Favored : 81.28 % 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 are not related in a simple way. whole: -0.24 (0.20), residues: 1848 helix: 1.02 (0.17), residues: 984 sheet: -1.08 (0.36), residues: 200 loop : -1.63 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 440 TYR 0.028 0.002 TYR B 249 PHE 0.021 0.002 PHE B 600 TRP 0.015 0.002 TRP A 414 HIS 0.004 0.001 HIS C 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (16176) covalent geometry : angle 0.69503 / 0.37 (21916) SS BOND : bond 0.00787 / 0.45 ( 4) SS BOND : angle 3.66095 / 1.79 ( 8) hydrogen bonds : bond 0.05965 / 3.80 ( 797) hydrogen bonds : angle 4.16674 / 2.82 ( 2415) Misc. bond : bond 0.00207 / 0.14 ( 4) link_NAG-ASN : bond 0.00240 / 0.15 ( 12) link_NAG-ASN : angle 2.27994 / 1.41 ( 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 333 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 266 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8119 (t80) cc_final: 0.7536 (t80) REVERT: A 252 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8193 (mpp) REVERT: A 305 ASN cc_start: 0.7482 (p0) cc_final: 0.7032 (p0) REVERT: A 583 MET cc_start: 0.6179 (OUTLIER) cc_final: 0.4859 (tpt) REVERT: A 631 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7197 (mt-10) REVERT: A 651 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: A 684 TYR cc_start: 0.5198 (OUTLIER) cc_final: 0.3192 (m-10) REVERT: B 252 MET cc_start: 0.8688 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: B 305 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6912 (p0) REVERT: B 312 GLU cc_start: 0.8407 (pm20) cc_final: 0.8191 (pm20) REVERT: B 583 MET cc_start: 0.6282 (pmm) cc_final: 0.5395 (tpt) REVERT: B 602 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8078 (pp) REVERT: B 631 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7475 (mt-10) REVERT: B 651 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7698 (tm-30) REVERT: C 252 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8173 (mpp) REVERT: C 583 MET cc_start: 0.6010 (pmm) cc_final: 0.5040 (tpt) REVERT: C 587 SER cc_start: 0.7330 (OUTLIER) cc_final: 0.7123 (p) REVERT: C 590 MET cc_start: 0.4839 (mtp) cc_final: 0.4185 (mtm) REVERT: C 603 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7497 (ttt) REVERT: C 631 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7462 (mt-10) REVERT: C 650 GLU cc_start: 0.8393 (tp30) cc_final: 0.7833 (pt0) REVERT: C 651 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: D 252 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8172 (mpp) REVERT: D 305 ASN cc_start: 0.7030 (OUTLIER) cc_final: 0.6655 (p0) REVERT: D 508 ASN cc_start: 0.8679 (m110) cc_final: 0.8478 (m110) REVERT: D 583 MET cc_start: 0.5883 (pmm) cc_final: 0.5075 (tpt) REVERT: D 602 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7951 (pp) REVERT: D 631 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7484 (mt-10) outliers start: 67 outliers final: 13 residues processed: 295 average time/residue: 0.4026 time to fit residues: 135.7030 Evaluate side-chains 272 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 482 PHE 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 482 PHE Chi-restraints excluded: chain C residue 587 SER 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 482 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: 5.9990 chunk 177 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 133 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN A 543 ASN B 255 GLN B 305 ASN B 543 ASN C 543 ASN D 255 GLN D 305 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 = 0.3848 r_free = 0.3848 target = 0.160010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.111140 restraints weight = 18467.274| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.26 r_work: 0.3105 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2079 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= 0.129 Angle : 0.592 7.484 21960 Z= 0.316 Chirality : 0.041 0.155 2456 Planarity : 0.006 0.220 2696 Dihedral : 8.788 85.115 2462 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.22 % Favored : 93.56 % Rotamer: Outliers : 3.08 % Allowed : 16.88 % Favored : 80.04 % 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 are not related in a simple way. whole: 0.02 (0.20), residues: 1848 helix: 1.37 (0.17), residues: 960 sheet: -1.01 (0.37), residues: 200 loop : -1.63 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG D 440 TYR 0.017 0.001 TYR B 527 PHE 0.022 0.001 PHE A 670 TRP 0.012 0.001 TRP D 414 HIS 0.001 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (16176) covalent geometry : angle 0.58667 / 0.31 (21916) SS BOND : bond 0.00402 / 0.23 ( 4) SS BOND : angle 2.46439 / 1.21 ( 8) hydrogen bonds : bond 0.04631 / 2.94 ( 797) hydrogen bonds : angle 3.88771 / 2.63 ( 2415) Misc. bond : bond 0.00339 / 0.24 ( 4) link_NAG-ASN : bond 0.00121 / 0.08 ( 12) link_NAG-ASN : angle 1.67790 / 1.07 ( 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 324 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 272 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8028 (t80) cc_final: 0.7648 (t80) REVERT: A 251 ARG cc_start: 0.8918 (ttt90) cc_final: 0.8679 (ttt90) REVERT: A 305 ASN cc_start: 0.7427 (p0) cc_final: 0.7037 (p0) REVERT: A 583 MET cc_start: 0.6038 (pmt) cc_final: 0.4778 (tpt) REVERT: A 602 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7962 (pp) REVERT: A 631 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7187 (mt-10) REVERT: A 651 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: A 684 TYR cc_start: 0.5105 (OUTLIER) cc_final: 0.3131 (m-10) REVERT: B 227 TYR cc_start: 0.8062 (t80) cc_final: 0.7586 (t80) REVERT: B 305 ASN cc_start: 0.7051 (OUTLIER) cc_final: 0.6396 (p0) REVERT: B 583 MET cc_start: 0.6264 (pmm) cc_final: 0.5376 (tpt) REVERT: B 651 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7641 (tm-30) REVERT: C 251 ARG cc_start: 0.8907 (ttt90) cc_final: 0.8661 (ttt90) REVERT: C 252 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8129 (mpp) REVERT: C 583 MET cc_start: 0.6116 (pmm) cc_final: 0.5095 (tpt) REVERT: C 590 MET cc_start: 0.4546 (mtp) cc_final: 0.3291 (mmt) REVERT: C 603 MET cc_start: 0.7486 (ttp) cc_final: 0.7129 (ttt) REVERT: C 651 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7475 (tm-30) REVERT: D 305 ASN cc_start: 0.7341 (OUTLIER) cc_final: 0.6955 (p0) REVERT: D 583 MET cc_start: 0.5684 (pmm) cc_final: 0.4853 (tpt) outliers start: 52 outliers final: 16 residues processed: 295 average time/residue: 0.4045 time to fit residues: 136.0444 Evaluate side-chains 267 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 243 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ARG 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 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 624 ASP Chi-restraints excluded: chain B residue 651 GLU 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 624 ASP Chi-restraints excluded: chain C residue 651 GLU Chi-restraints excluded: chain C residue 677 LEU Chi-restraints excluded: chain D residue 263 SER 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 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: 3.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 151 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 305 ASN B 543 ASN C 543 ASN D 305 ASN D 508 ASN D 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108315 restraints weight = 18557.526| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.28 r_work: 0.3081 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16196 Z= 0.171 Angle : 0.639 8.468 21960 Z= 0.338 Chirality : 0.043 0.158 2456 Planarity : 0.007 0.285 2696 Dihedral : 8.725 85.466 2462 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.98 % Favored : 92.80 % Rotamer: Outliers : 4.15 % Allowed : 16.88 % Favored : 78.97 % 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 are not related in a simple way. whole: 0.02 (0.20), residues: 1848 helix: 1.36 (0.17), residues: 964 sheet: -1.05 (0.37), residues: 200 loop : -1.63 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 440 TYR 0.018 0.002 TYR B 249 PHE 0.021 0.002 PHE B 600 TRP 0.012 0.001 TRP C 414 HIS 0.002 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (16176) covalent geometry : angle 0.63295 / 0.34 (21916) SS BOND : bond 0.00603 / 0.34 ( 4) SS BOND : angle 2.66141 / 1.33 ( 8) hydrogen bonds : bond 0.05098 / 3.23 ( 797) hydrogen bonds : angle 3.93154 / 2.66 ( 2415) Misc. bond : bond 0.00304 / 0.22 ( 4) link_NAG-ASN : bond 0.00092 / 0.06 ( 12) link_NAG-ASN : angle 1.91231 / 1.19 ( 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 326 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 256 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.8049 (t80) cc_final: 0.7670 (t80) REVERT: A 252 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8182 (mpp) REVERT: A 305 ASN cc_start: 0.7392 (p0) cc_final: 0.6912 (p0) REVERT: A 583 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.4657 (tpt) REVERT: A 590 MET cc_start: 0.6419 (mmt) cc_final: 0.6079 (ptm) REVERT: A 602 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7680 (pp) REVERT: A 631 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 651 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7494 (tm-30) REVERT: A 684 TYR cc_start: 0.5079 (OUTLIER) cc_final: 0.3108 (m-10) REVERT: B 227 TYR cc_start: 0.8105 (t80) cc_final: 0.7594 (t80) REVERT: B 251 ARG cc_start: 0.8907 (ttt90) cc_final: 0.8650 (ttt90) REVERT: B 252 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8212 (mpp) REVERT: B 305 ASN cc_start: 0.6999 (OUTLIER) cc_final: 0.6331 (p0) REVERT: B 583 MET cc_start: 0.6193 (pmm) cc_final: 0.5101 (tpt) REVERT: B 602 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7970 (pp) REVERT: B 651 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7652 (tm-30) REVERT: C 251 ARG cc_start: 0.8939 (ttt90) cc_final: 0.8688 (ttt90) REVERT: C 252 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: C 305 ASN cc_start: 0.6853 (p0) cc_final: 0.6087 (p0) REVERT: C 583 MET cc_start: 0.6086 (pmm) cc_final: 0.4912 (tpt) REVERT: C 590 MET cc_start: 0.4667 (mtp) cc_final: 0.3764 (ptm) REVERT: C 602 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7817 (pp) REVERT: C 603 MET cc_start: 0.7682 (ttp) cc_final: 0.7231 (ttt) REVERT: C 651 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: D 252 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8184 (mpp) REVERT: D 305 ASN cc_start: 0.7264 (OUTLIER) cc_final: 0.6749 (p0) REVERT: D 583 MET cc_start: 0.5846 (pmm) cc_final: 0.4868 (tpt) REVERT: D 590 MET cc_start: 0.5944 (ptt) cc_final: 0.5156 (ppp) REVERT: D 603 MET cc_start: 0.7599 (ttp) cc_final: 0.7181 (ttt) outliers start: 70 outliers final: 31 residues processed: 288 average time/residue: 0.4054 time to fit residues: 133.4603 Evaluate side-chains 287 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 242 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 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 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 263 SER Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 350 VAL 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 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 464 ARG 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 653 ASN 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 305 ASN 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 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: 0.9980 chunk 139 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 305 ASN B 543 ASN C 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.161464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.112427 restraints weight = 18465.092| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.27 r_work: 0.3131 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16196 Z= 0.121 Angle : 0.573 7.244 21960 Z= 0.306 Chirality : 0.041 0.141 2456 Planarity : 0.005 0.185 2696 Dihedral : 8.175 86.192 2462 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.49 % Favored : 93.29 % Rotamer: Outliers : 3.02 % Allowed : 18.54 % Favored : 78.44 % 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 are not related in a simple way. whole: 0.16 (0.20), residues: 1848 helix: 1.55 (0.17), residues: 956 sheet: -0.96 (0.37), residues: 200 loop : -1.65 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 440 TYR 0.016 0.001 TYR B 527 PHE 0.024 0.001 PHE A 670 TRP 0.011 0.001 TRP C 414 HIS 0.001 0.000 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (16176) covalent geometry : angle 0.56931 / 0.30 (21916) SS BOND : bond 0.00386 / 0.22 ( 4) SS BOND : angle 1.92023 / 0.97 ( 8) hydrogen bonds : bond 0.04285 / 2.71 ( 797) hydrogen bonds : angle 3.76617 / 2.54 ( 2415) Misc. bond : bond 0.00181 / 0.13 ( 4) link_NAG-ASN : bond 0.00113 / 0.07 ( 12) link_NAG-ASN : angle 1.57491 / 1.00 ( 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 319 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 268 time to evaluate : 0.586 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: 0.7978 (t80) cc_final: 0.7702 (t80) REVERT: A 252 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8194 (mpp) REVERT: A 305 ASN cc_start: 0.7298 (p0) cc_final: 0.6902 (p0) REVERT: A 583 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.4954 (tpt) REVERT: A 590 MET cc_start: 0.6611 (mmt) cc_final: 0.6338 (pp-130) REVERT: A 651 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: A 684 TYR cc_start: 0.5031 (OUTLIER) cc_final: 0.3146 (m-10) REVERT: B 251 ARG cc_start: 0.8859 (ttt90) cc_final: 0.8634 (ttt90) REVERT: B 252 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8160 (mpp) REVERT: B 305 ASN cc_start: 0.7115 (OUTLIER) cc_final: 0.6324 (p0) REVERT: B 343 GLU cc_start: 0.8486 (mp0) cc_final: 0.7962 (mm-30) REVERT: B 455 TRP cc_start: 0.8434 (OUTLIER) cc_final: 0.7787 (p90) REVERT: B 583 MET cc_start: 0.5990 (pmm) cc_final: 0.4958 (tpp) REVERT: B 590 MET cc_start: 0.3854 (mtp) cc_final: 0.3235 (mtm) REVERT: B 602 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7943 (pp) REVERT: B 651 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: C 251 ARG cc_start: 0.8854 (ttt90) cc_final: 0.8628 (ttt90) REVERT: C 252 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8138 (mpp) REVERT: C 305 ASN cc_start: 0.6994 (p0) cc_final: 0.6113 (p0) REVERT: C 583 MET cc_start: 0.5938 (pmm) cc_final: 0.4841 (tpt) REVERT: C 590 MET cc_start: 0.4595 (mtp) cc_final: 0.3644 (ptm) REVERT: C 602 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7774 (pp) REVERT: C 603 MET cc_start: 0.7591 (ttp) cc_final: 0.7082 (ttt) REVERT: C 651 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7412 (tm-30) REVERT: D 251 ARG cc_start: 0.8861 (ttt90) cc_final: 0.8646 (ttt90) REVERT: D 252 MET cc_start: 0.8804 (OUTLIER) cc_final: 0.8154 (mpp) REVERT: D 305 ASN cc_start: 0.7283 (OUTLIER) cc_final: 0.6754 (p0) REVERT: D 583 MET cc_start: 0.5964 (pmm) cc_final: 0.5015 (tpt) REVERT: D 590 MET cc_start: 0.6055 (ptt) cc_final: 0.5156 (ppp) REVERT: D 600 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7219 (p90) REVERT: D 603 MET cc_start: 0.7544 (ttp) cc_final: 0.7011 (ttt) outliers start: 51 outliers final: 21 residues processed: 287 average time/residue: 0.4570 time to fit residues: 149.4459 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 : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 425 ASP Chi-restraints excluded: chain A residue 464 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 305 ASN 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 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 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 305 ASN Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 600 PHE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 54 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 180 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 305 ASN B 543 ASN C 543 ASN D 305 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.162111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.113550 restraints weight = 18330.281| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.24 r_work: 0.3147 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16196 Z= 0.116 Angle : 0.583 10.463 21960 Z= 0.308 Chirality : 0.041 0.151 2456 Planarity : 0.004 0.126 2696 Dihedral : 7.912 88.675 2462 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.87 % Favored : 92.97 % Rotamer: Outliers : 2.67 % Allowed : 19.55 % Favored : 77.78 % 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 are not related in a simple way. whole: 0.24 (0.20), residues: 1848 helix: 1.62 (0.17), residues: 956 sheet: -0.92 (0.37), residues: 200 loop : -1.63 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 417 TYR 0.014 0.001 TYR B 527 PHE 0.022 0.001 PHE B 600 TRP 0.010 0.001 TRP D 414 HIS 0.002 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (16176) covalent geometry : angle 0.57955 / 0.31 (21916) SS BOND : bond 0.00364 / 0.20 ( 4) SS BOND : angle 1.78881 / 0.90 ( 8) hydrogen bonds : bond 0.04095 / 2.58 ( 797) hydrogen bonds : angle 3.71125 / 2.50 ( 2415) Misc. bond : bond 0.00107 / 0.08 ( 4) link_NAG-ASN : bond 0.00111 / 0.07 ( 12) link_NAG-ASN : angle 1.50832 / 0.96 ( 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 291 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 246 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 TYR cc_start: 0.7921 (t80) cc_final: 0.7715 (t80) REVERT: A 305 ASN cc_start: 0.7294 (p0) cc_final: 0.6910 (p0) REVERT: A 583 MET cc_start: 0.6025 (OUTLIER) cc_final: 0.4669 (tpt) REVERT: A 590 MET cc_start: 0.6616 (mmt) cc_final: 0.6386 (pp-130) REVERT: B 229 LEU cc_start: 0.8506 (mt) cc_final: 0.8249 (mp) REVERT: B 251 ARG cc_start: 0.8800 (ttt90) cc_final: 0.8578 (ttt90) REVERT: B 252 MET cc_start: 0.8772 (OUTLIER) cc_final: 0.8125 (mpp) REVERT: B 305 ASN cc_start: 0.7079 (OUTLIER) cc_final: 0.6236 (p0) REVERT: B 343 GLU cc_start: 0.8437 (mp0) cc_final: 0.7955 (mm-30) REVERT: B 455 TRP cc_start: 0.8366 (OUTLIER) cc_final: 0.7733 (p90) REVERT: B 583 MET cc_start: 0.5830 (pmm) cc_final: 0.4878 (tpp) REVERT: B 590 MET cc_start: 0.3883 (mtp) cc_final: 0.3485 (mtm) REVERT: B 602 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7845 (pp) REVERT: C 251 ARG cc_start: 0.8840 (ttt90) cc_final: 0.8612 (ttt90) REVERT: C 255 GLN cc_start: 0.8814 (mt0) cc_final: 0.8605 (mt0) REVERT: C 305 ASN cc_start: 0.6839 (p0) cc_final: 0.5978 (p0) REVERT: C 583 MET cc_start: 0.5906 (pmm) cc_final: 0.4735 (tpt) REVERT: C 590 MET cc_start: 0.4800 (mtp) cc_final: 0.3463 (ptm) REVERT: C 603 MET cc_start: 0.7514 (ttp) cc_final: 0.7097 (ttt) REVERT: D 252 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8116 (mpp) REVERT: D 305 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6811 (p0) REVERT: D 312 GLU cc_start: 0.8099 (pm20) cc_final: 0.7866 (pm20) REVERT: D 343 GLU cc_start: 0.8464 (mp0) cc_final: 0.7933 (mm-30) REVERT: D 583 MET cc_start: 0.5895 (pmm) cc_final: 0.5102 (tpt) REVERT: D 590 MET cc_start: 0.5862 (ptt) cc_final: 0.5036 (ppp) REVERT: D 603 MET cc_start: 0.7405 (ttp) cc_final: 0.6910 (ttt) outliers start: 45 outliers final: 18 residues processed: 264 average time/residue: 0.4564 time to fit residues: 137.5075 Evaluate side-chains 260 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 235 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 252 MET Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 425 ASP 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 B residue 677 LEU 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 624 ASP Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 305 ASN 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 586 LEU Chi-restraints excluded: chain D residue 624 ASP 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: 0.9980 chunk 162 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 97 optimal weight: 0.7980 chunk 158 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 255 GLN A 543 ASN B 305 ASN B 543 ASN C 543 ASN D 543 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.157996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.108423 restraints weight = 18571.940| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.25 r_work: 0.3084 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16196 Z= 0.179 Angle : 0.646 8.893 21960 Z= 0.340 Chirality : 0.044 0.180 2456 Planarity : 0.005 0.154 2696 Dihedral : 8.232 89.659 2460 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 2.84 % Allowed : 19.61 % Favored : 77.55 % 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 are not related in a simple way. whole: 0.18 (0.20), residues: 1848 helix: 1.44 (0.17), residues: 976 sheet: -1.02 (0.37), residues: 200 loop : -1.51 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 440 TYR 0.015 0.002 TYR A 249 PHE 0.028 0.002 PHE A 670 TRP 0.008 0.001 TRP A 554 HIS 0.003 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (16176) covalent geometry : angle 0.63978 / 0.34 (21916) SS BOND : bond 0.00673 / 0.37 ( 4) SS BOND : angle 2.76205 / 1.37 ( 8) hydrogen bonds : bond 0.05099 / 3.23 ( 797) hydrogen bonds : angle 3.85816 / 2.60 ( 2415) Misc. bond : bond 0.00165 / 0.12 ( 4) link_NAG-ASN : bond 0.00144 / 0.10 ( 12) link_NAG-ASN : angle 1.98686 / 1.21 ( 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 304 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.588 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: 0.7983 (t80) cc_final: 0.7675 (t80) REVERT: A 252 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8108 (mpp) REVERT: A 305 ASN cc_start: 0.7331 (p0) cc_final: 0.6889 (p0) REVERT: A 583 MET cc_start: 0.5870 (OUTLIER) cc_final: 0.4545 (tpt) REVERT: A 590 MET cc_start: 0.6645 (mmt) cc_final: 0.6343 (ptm) REVERT: A 602 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7834 (tp) REVERT: A 631 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7324 (mt-10) REVERT: B 251 ARG cc_start: 0.8889 (ttt90) cc_final: 0.8644 (ttt90) REVERT: B 252 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8170 (mpp) REVERT: B 305 ASN cc_start: 0.7157 (OUTLIER) cc_final: 0.6222 (p0) REVERT: B 455 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.7780 (p90) REVERT: B 583 MET cc_start: 0.6031 (pmm) cc_final: 0.4985 (tpp) REVERT: B 590 MET cc_start: 0.4012 (mtp) cc_final: 0.3534 (mtm) REVERT: B 602 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7901 (pp) REVERT: C 295 MET cc_start: 0.5353 (ppp) cc_final: 0.5123 (ppp) REVERT: C 305 ASN cc_start: 0.6825 (p0) cc_final: 0.5913 (p0) REVERT: C 508 ASN cc_start: 0.8682 (m110) cc_final: 0.8333 (m-40) REVERT: C 583 MET cc_start: 0.5897 (pmm) cc_final: 0.4700 (tpt) REVERT: C 590 MET cc_start: 0.4752 (mtp) cc_final: 0.3409 (ptm) REVERT: C 603 MET cc_start: 0.7614 (ttp) cc_final: 0.7089 (ttt) REVERT: D 252 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8152 (mpp) REVERT: D 583 MET cc_start: 0.5953 (pmm) cc_final: 0.5049 (tpt) REVERT: D 590 MET cc_start: 0.5845 (ptt) cc_final: 0.5023 (ppp) REVERT: D 602 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7882 (pp) REVERT: D 603 MET cc_start: 0.7492 (ttp) cc_final: 0.6977 (ttt) REVERT: D 609 LEU cc_start: 0.8702 (mt) cc_final: 0.8459 (mp) outliers start: 48 outliers final: 23 residues processed: 278 average time/residue: 0.4455 time to fit residues: 141.0788 Evaluate side-chains 270 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 500 LEU 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 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 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 602 ILE Chi-restraints excluded: chain B residue 624 ASP Chi-restraints excluded: chain B residue 677 LEU 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 624 ASP Chi-restraints excluded: chain C residue 653 ASN 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 602 ILE Chi-restraints excluded: chain D residue 624 ASP Chi-restraints excluded: chain D residue 683 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 178 optimal weight: 0.0980 chunk 174 optimal weight: 0.0970 chunk 110 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 305 ASN B 543 ASN 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 = 0.3890 r_free = 0.3890 target = 0.164027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115252 restraints weight = 18525.264| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.27 r_work: 0.3184 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16196 Z= 0.112 Angle : 0.580 13.017 21960 Z= 0.305 Chirality : 0.041 0.183 2456 Planarity : 0.004 0.045 2696 Dihedral : 7.712 88.071 2460 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.13 % Allowed : 20.62 % Favored : 77.25 % 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 are not related in a simple way. whole: 0.31 (0.20), residues: 1848 helix: 1.68 (0.17), residues: 956 sheet: -0.84 (0.38), residues: 200 loop : -1.61 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 251 TYR 0.009 0.001 TYR A 249 PHE 0.023 0.001 PHE B 600 TRP 0.010 0.001 TRP D 414 HIS 0.001 0.000 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (16176) covalent geometry : angle 0.57716 / 0.30 (21916) SS BOND : bond 0.00221 / 0.12 ( 4) SS BOND : angle 1.46515 / 0.74 ( 8) hydrogen bonds : bond 0.03815 / 2.40 ( 797) hydrogen bonds : angle 3.68364 / 2.48 ( 2415) Misc. bond : bond 0.00042 / 0.02 ( 4) link_NAG-ASN : bond 0.00213 / 0.14 ( 12) link_NAG-ASN : angle 1.40695 / 0.91 ( 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 293 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 257 time to evaluate : 0.537 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 305 ASN cc_start: 0.7242 (p0) cc_final: 0.6820 (p0) REVERT: A 343 GLU cc_start: 0.8346 (mp0) cc_final: 0.7836 (mm-30) REVERT: A 538 PHE cc_start: 0.8163 (t80) cc_final: 0.7899 (t80) REVERT: A 583 MET cc_start: 0.5807 (OUTLIER) cc_final: 0.4569 (tpt) REVERT: A 590 MET cc_start: 0.6833 (mmt) cc_final: 0.6551 (pp-130) REVERT: A 602 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7656 (tp) REVERT: B 252 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8065 (mpp) REVERT: B 343 GLU cc_start: 0.8347 (mp0) cc_final: 0.7824 (mm-30) REVERT: B 455 TRP cc_start: 0.8415 (OUTLIER) cc_final: 0.7766 (p90) REVERT: B 583 MET cc_start: 0.5797 (pmm) cc_final: 0.4866 (tpp) REVERT: B 590 MET cc_start: 0.3996 (mtp) cc_final: 0.3555 (mtm) REVERT: B 602 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7724 (tp) REVERT: C 252 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8042 (mpp) REVERT: C 305 ASN cc_start: 0.7208 (p0) cc_final: 0.6222 (p0) REVERT: C 583 MET cc_start: 0.5587 (pmm) cc_final: 0.4568 (tpt) REVERT: C 590 MET cc_start: 0.4488 (mtp) cc_final: 0.3351 (ptm) REVERT: C 602 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7782 (pp) REVERT: D 312 GLU cc_start: 0.8068 (pm20) cc_final: 0.7807 (pm20) REVERT: D 343 GLU cc_start: 0.8356 (mp0) cc_final: 0.7822 (mm-30) REVERT: D 583 MET cc_start: 0.5820 (pmm) cc_final: 0.4998 (tpt) REVERT: D 590 MET cc_start: 0.5860 (ptt) cc_final: 0.5028 (ppp) REVERT: D 603 MET cc_start: 0.7463 (ttp) cc_final: 0.7192 (ttm) outliers start: 36 outliers final: 14 residues processed: 270 average time/residue: 0.3986 time to fit residues: 123.4604 Evaluate side-chains 258 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP 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 B residue 252 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 252 MET 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 653 ASN Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU 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 181 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 125 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 151 optimal weight: 0.0270 chunk 57 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 255 GLN B 543 ASN C 255 GLN C 543 ASN D 255 GLN D 543 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.165718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.117545 restraints weight = 18572.070| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.27 r_work: 0.3211 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16196 Z= 0.111 Angle : 0.589 12.796 21960 Z= 0.308 Chirality : 0.041 0.186 2456 Planarity : 0.004 0.044 2696 Dihedral : 7.409 85.080 2460 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.72 % Allowed : 21.86 % Favored : 76.42 % 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 are not related in a simple way. whole: 0.34 (0.20), residues: 1848 helix: 1.68 (0.17), residues: 960 sheet: -0.78 (0.37), residues: 200 loop : -1.61 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 251 TYR 0.012 0.001 TYR A 227 PHE 0.028 0.001 PHE A 670 TRP 0.008 0.001 TRP C 414 HIS 0.002 0.000 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (16176) covalent geometry : angle 0.58642 / 0.31 (21916) SS BOND : bond 0.00292 / 0.19 ( 4) SS BOND : angle 1.39977 / 0.69 ( 8) hydrogen bonds : bond 0.03580 / 2.26 ( 797) hydrogen bonds : angle 3.63106 / 2.44 ( 2415) Misc. bond : bond 0.00042 / 0.02 ( 4) link_NAG-ASN : bond 0.00168 / 0.10 ( 12) link_NAG-ASN : angle 1.35222 / 0.87 ( 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 285 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 ASN cc_start: 0.7268 (p0) cc_final: 0.6851 (p0) REVERT: A 343 GLU cc_start: 0.8349 (mp0) cc_final: 0.7850 (mm-30) REVERT: A 538 PHE cc_start: 0.8123 (t80) cc_final: 0.7886 (t80) REVERT: A 583 MET cc_start: 0.5779 (OUTLIER) cc_final: 0.4552 (tpt) REVERT: A 590 MET cc_start: 0.6673 (mmt) cc_final: 0.6435 (ptm) REVERT: A 602 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7661 (tp) REVERT: B 343 GLU cc_start: 0.8286 (mp0) cc_final: 0.7801 (mm-30) REVERT: B 455 TRP cc_start: 0.8385 (OUTLIER) cc_final: 0.7813 (p90) REVERT: B 538 PHE cc_start: 0.8091 (t80) cc_final: 0.7809 (t80) REVERT: B 583 MET cc_start: 0.5846 (pmm) cc_final: 0.4934 (tpp) REVERT: B 590 MET cc_start: 0.4200 (mtp) cc_final: 0.3746 (mtm) REVERT: B 602 ILE cc_start: 0.8077 (OUTLIER) cc_final: 0.7657 (tp) REVERT: B 631 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7454 (tp30) REVERT: C 305 ASN cc_start: 0.7008 (p0) cc_final: 0.6065 (p0) REVERT: C 583 MET cc_start: 0.5576 (pmm) cc_final: 0.4605 (tpp) REVERT: C 590 MET cc_start: 0.4355 (mtp) cc_final: 0.3394 (ptm) REVERT: C 631 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7469 (tp30) REVERT: D 343 GLU cc_start: 0.8119 (mp0) cc_final: 0.7680 (mm-30) REVERT: D 583 MET cc_start: 0.5850 (pmm) cc_final: 0.4952 (tpt) REVERT: D 603 MET cc_start: 0.7306 (ttp) cc_final: 0.6824 (ttt) REVERT: D 631 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7438 (tp30) REVERT: D 675 MET cc_start: 0.6980 (ppp) cc_final: 0.6728 (ppp) outliers start: 29 outliers final: 10 residues processed: 269 average time/residue: 0.4272 time to fit residues: 131.6400 Evaluate side-chains 252 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 ASP 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 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 535 LEU Chi-restraints excluded: chain D residue 482 PHE Chi-restraints excluded: chain D residue 535 LEU Chi-restraints excluded: chain D residue 586 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 94 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 154 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 543 ASN B 305 ASN B 543 ASN 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 = 0.3846 r_free = 0.3846 target = 0.160172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.110816 restraints weight = 18429.791| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.25 r_work: 0.3122 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16196 Z= 0.148 Angle : 0.638 12.148 21960 Z= 0.335 Chirality : 0.043 0.187 2456 Planarity : 0.004 0.053 2696 Dihedral : 7.736 87.240 2460 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.93 % Favored : 92.86 % Rotamer: Outliers : 1.66 % Allowed : 22.22 % Favored : 76.13 % 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 are not related in a simple way. whole: 0.36 (0.20), residues: 1848 helix: 1.66 (0.17), residues: 956 sheet: -0.86 (0.37), residues: 200 loop : -1.48 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 251 TYR 0.014 0.001 TYR C 249 PHE 0.024 0.001 PHE C 485 TRP 0.009 0.001 TRP C 554 HIS 0.004 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16176) covalent geometry : angle 0.63267 / 0.33 (21916) SS BOND : bond 0.00582 / 0.33 ( 4) SS BOND : angle 2.69077 / 1.28 ( 8) hydrogen bonds : bond 0.04578 / 2.89 ( 797) hydrogen bonds : angle 3.75569 / 2.53 ( 2415) Misc. bond : bond 0.00056 / 0.03 ( 4) link_NAG-ASN : bond 0.00047 / 0.03 ( 12) link_NAG-ASN : angle 1.70868 / 1.06 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4853.19 seconds wall clock time: 83 minutes 34.50 seconds (5014.50 seconds total)